Rapid analysis of variations in a genome

ABSTRACT

The invention provides a method useful for determining the sequence of large numbers of loci of interest on a single or multiple chromosomes. The method utilizes an oligonucleotide primer that contains a recognition site for a restriction enzyme such that digestion with the restriction enzyme generates a 5′ overhang containing the locus of interest. The 5′ overhang is used as a template to incorporate nucleotides, which can be detected. The method is especially amenable to the analysis of large numbers of sequences, such as single nucleotide polymorphisms, from one sample of nucleic acid.

This appln claims benefit of 60/360,232 Mar. 1, 2002.

BACKGROUND OF THE INVENTION

1. Field of the Invention

The present invention is directed to a rapid method for determining thesequence of nucleic acid. The method is especially useful forgenotyping, and for the detection of one to tens to hundreds tothousands of single nucleotide polymorphisms (SNPs) or mutations onsingle or on multiple chromosomes, and for the detection of chromosomalabnormalities, such as truncations, transversions, trisomies, andmonosomies.

2. Background Art

Sequence variation among individuals comprises a continuum fromdeleterious disease mutations to neutral polymorphisms. There are morethan three thousand genetic diseases currently known including DuchenneMuscular Dystrophy, Alzheimer's Disease, Cystic Fibrosis, andHuntington's Disease (D. N. Cooper and M. Krawczak, “Human GenomeMutations,” BIOS Scientific Publishers, Oxford (1993)). Also, particularDNA sequences may predispose individuals to a variety of diseases suchas obesity, arteriosclerosis, and various types of cancer, includingbreast, prostate, and colon. In addition, chromosomal abnormalities,such as trisomy 21, which results in Down's Syndrome, trisomy 18, whichresults in Edward's Syndrome, trisomy 13, which results in PatauSyndrome, monosomy X, which results in Turner's Syndrome, and other sexaneuploidies, account for a significant portion of the genetic defectsin liveborn human beings. Knowledge of gene mutations, chromosomalabnormalities, and variations in gene sequences, such as singlenucleotide polymorphisms (SNPs), will help to understand, diagnose,prevent, and treat diseases.

Most frequently, sequence variation is seen in differences in thelengths of repeated sequence elements, such as minisatellites andmicrosatellites, as small insertions or deletions, and as substitutionsof the individual bases. Single nucleotide polymorphisms (SNPs)represent the most common form of sequence variation; three millioncommon SNPs with a population frequency of over 5% have been estimatedto be present in the human genome. Small deletions or insertions, whichusually cause frameshift mutations, occur on average, once in every 12kilobases of genomic DNA (Wang, D. G. et al., Science 280: 1077-1082(1998)). A genetic map using these polymorphisms as a guide is beingdeveloped (http://research.marshfieldclinic.org/genetics/; internetaddress as of Jan. 10, 2002).

The nucleic acid sequence of the human genome was published in February,2001, and provides a genetic map of unprecedented resolution, containingseveral hundred thousand SNP markers, and a potential wealth ofinformation on human diseases (Venter et al., Science 291:1304-1351(2001); International Human Genome Sequencing Consortium, Nature409:860-921 (2001)). However, the length of DNA contained within thehuman chromosomes totals over 3 billion base pairs so sequencing thegenome of every individual is impractical. Thus, it is imperative todevelop high throughput methods for rapidly determining the presence ofallelic variants of SNPs and point mutations, which predispose to orcause disease phenotypes. Efficient methods to characterize functionalpolymorphisms that affect an individual's physiology, psychology,audiology, ophthalmology, neurology, response to drugs, drug metabolism,and drug interactions also are needed.

Several techniques are widely used for analyzing and detecting geneticvariations, such as DNA sequencing, restriction fragment lengthpolymorphisms (RFLP), DNA hybridization assays, including DNAmicroarrays and peptide nucleic acid analysis, and the ProteinTruncation Test (PTT), all of which have limitations. Although DNAsequencing is the most definitive method, it is also the most timeconsuming and expensive. Often, the entire coding sequence of a gene isanalyzed even though only a small fraction of the coding sequence is ofinterest. In most instances, a limited number of mutations in anyparticular gene account for the majority of the disease phenotypes.

For example, the cystic fibrosis transmembrane conductance regulator(CFTR) gene is composed of 24 exons spanning over 250,000 base pairs(Rommens et al., Science 245:1059-1065 (1989); Riordan et al., Science245:1066-73 (1989)). Currently, there are approximately 200 mutations inthe CFTR gene that are associated with a disease state of CysticFibrosis. Therefore, only a very small percentage of the reading framefor the CFTR gene needs to be analyzed. Furthermore, a total of 10mutations make up 75.1% of all known disease cases. The deletion of asingle phenylalanine residue, F508, accounts for 66% of all CysticFibrosis cases in Caucasians.

Hybridization techniques, including Southern Blots, Slot Blots, DotBlots, and DNA microarrays, are commonly used to detect geneticvariations (Molecular Cloning, A Laboratory Manual, Cold Spring HarborLaboratory Press, Third Edition (2001). In a typical hybridizationassay, an unknown nucleotide sequence (“the target”) is analyzed basedon its affinity for another fragment with a known nucleotide sequence(“the probe”). If the two fragments hybridize under “stringentconditions,” the sequences are thought to be complementary, and thesequence of the target fragment may be inferred from “the probe”sequence.

However, the results from a typical hybridization assay often aredifficult to interpret. The absence or presence of a hybridizationsignal is dependent upon the definition of “stringent conditions.” Anynumber of variables may be used to raise or lower stringency conditionssuch as salt concentration, the presence or absence of competitornucleotide fragments, the number of washes performed to removenon-specific binding and the time and temperature at which thehybridizations are performed. Commonly, hybridization conditions must beoptimized for each “target” nucleotide fragment, which istime-consuming, and inconsistent with a high throughput method. A highdegree of variability is often seen in hybridization assays, as well asa high proportion of false positives. Typically, hybridization assaysfunction as a screen for likely candidates but a positive confirmationrequires DNA sequencing analysis.

Several techniques for the detection of mutations have evolved based onthe principal of hybridization analysis. For example, in the primerextension assay, the DNA region spanning the nucleotide of interest isamplified by PCR, or any other suitable amplification technique. Afteramplification, a primer is hybridized to a target nucleic acid sequence,wherein the last nucleotide of the 3′ end of the primer annealsimmediately 5′ to the nucleotide position on the target sequence that isto be analyzed. The annealed primer is extended by a single, labelednucleotide triphosphate. The incorporated nucleotide is then detected.

There are several limitations to the primer extension assay. First, theregion of interest must be amplified prior to primer extension, whichincreases the time and expense of the assay. Second, PCR primers anddNTPs must be completely removed before primer extension, and residualcontaminants can interfere with the proper analysis of the results.Third, and the most restrictive aspect of the assay, is that the primeris hybridized to the DNA template, which requires optimization ofconditions for each primer, and for each sequence that is analyzed.Hybridization assays have a low degree of reproducibility, and a highdegree of non-specificity.

The Peptide Nucleic Acid (PNA) affinity assay is a derivative oftraditional hybridization assays (Nielsen et al., Science 254:1497-1500(1991); Egholm et al., J. Am. Chem. Soc. 114:1895-1897 (1992); James etal., Protein Science 3:1347-1350 (1994)). PNAs are structural DNA mimicsthat follow Watson-Crick base pairing rules, and are used in standardDNA hybridization assays. PNAs display greater specificity inhybridization assays because a PNA/DNA mismatch is more destabilizingthan a DNA/DNA mismatch and complementary PNA/DNA strands form strongerbonds than complementary DNA/DNA strands. However, genetic analysisusing PNAs still requires a laborious hybridization step, and as such,is subject to a high degree of non-specificity and difficulty withreproducibility.

Recently, DNA microarrays have been developed to detect geneticvariations and polymorphisms (Taton et al., Science 289:1757-60, 2000;Lockhart et al., Nature 405:827-836 (2000); Gerhold et al., Trends inBiochemical Sciences 24:168-73 (1999); Wallace, R. W., MolecularMedicine Today 3:384-89 (1997); Blanchard and Hood, Nature Biotechnology149:1649 (1996)). DNA microarrays are fabricated by high-speed robotics,on glass or nylon substrates, and contain DNA fragments with knownidentities (“the probe”). The microarrays are used for matching knownand unknown DNA fragments (“the target”) based on traditionalbase-pairing rules. The advantage of DNA microarrays is that one DNAchip may provide information on thousands of genes simultaneously.However, DNA microarrays are still based on the principle ofhybridization, and as such, are subject to the disadvantages discussedabove.

The Protein Truncation Test (PTT) is also commonly used to detectgenetic polymorphisms (Roest et al., Human Molecular Genetics2:1719-1721, (1993); Van Der Luit et al., Genomics 20:1-4 (1994);Hogervorst et al., Nature Genetics 10: 208-212 (1995)). Typically, inthe PTT, the gene of interest is PCR amplified, subjected to in vitrotranscription/translation, purified, and analyzed by polyacrylamide gelelectrophoresis. The PTT is useful for screening large portions ofcoding sequence and detecting mutations that produce stop codons, whichsignificantly diminish the size of the expected protein. However, thePTT is not designed to detect mutations that do not significantly alterthe size of the protein.

Thus, a need still exists for a rapid method of analyzing DNA,especially genomic DNA suspected of having one or more single nucleotidepolymorphisms or mutations.

BRIEF SUMMARY OF THE INVENTION

The invention is directed to a method for determining a sequence of alocus of interest, the method comprising: (a) amplifying a locus ofinterest on a template DNA using a first and second primers, wherein thesecond primer contains a recognition site for a restriction enzyme suchthat digestion with the restriction enzyme generates a 5′ overhangcontaining the locus of interest; (b) digesting the amplified DNA withthe restriction enzyme that recognizes the recognition site on thesecond primer; (c) incorporating a nucleotide into the digested DNA of(b) by using the 5′ overhang containing the locus of interest as atemplate; and (d) determining the sequence of the locus of interest bydetermining the sequence of the DNA of (c).

The invention is also directed to a method for determining a sequence ofa locus of interest, said method comprising: (a) amplifying a locus ofinterest on a template DNA using a first and second primers, wherein thesecond primer contains a portion of a recognition site for a restrictionenzyme, wherein a full recognition site for the restriction enzyme isgenerated upon amplification of the template DNA such that digestionwith the restriction enzyme generates a 5′ overhang containing the locusof interest; (b) digesting the amplified DNA with the restriction enzymethat recognizes the full recognition site generated by the second primerand the template DNA; (c) incorporating a nucleotide into the digestedDNA of (b) by using the 5′ overhang containing the locus of interest asa template; and determining the sequence of the locus of interest bydetermining the sequence of the DNA of (c).

The template DNA can be obtained from any source including syntheticnucleic acid, preferably from a bacterium, fungus, virus, plant,protozoan, animal or human source. In one embodiment, the template DNAis obtained from a human source. In another embodiment, the template DNAis obtained from a cell, tissue, blood sample, serum sample, plasmasample, urine sample, spinal fluid, lymphatic fluid, semen, vaginalsecretion, ascitic fluid, saliva, mucosa secretion, peritoneal fluid,fecal sample, or body exudates.

The 3′ region of the first and/or second primer can contain a mismatchwith the template DNA. The mismatch can occur at but is not limited tothe last 1, 2, or 3 bases at the 3′ end.

The restriction enzyme used in the invention can cut DNA at therecognition site. The restriction enzyme can be but is not limited toPf1F I, Sau96 I, ScrF I, BsaJ I, Bssk I, Dde I, EcoN I, Fnu4H I, Hinf I,or Tth111 I. Alternatively, the restriction enzyme used in the inventioncan cut DNA at a distance from its recognition site.

In another embodiment, the first primer contains a recognition site fora restriction enzyme. In a preferred embodiment, the restriction enzymerecognition site is different from the restriction enzyme recognitionsite on the second primer. The invention includes digesting theamplified DNA with a restriction enzyme that recognizes the recognitionsite on the first primer.

Preferably, the recognition site on the second primer is for arestriction enzyme that cuts DNA at a distance from its recognition siteand generates a 5′ overhang, containing the locus of interest. In apreferred embodiment, the recognition site on the second primer is for aType IIS restriction enzyme. The Type IIS restriction enzyme, e.g., isselected from the group consisting of: Alw I, Alw26 I, Bbs I, Bbv I,BceA I, Bmr I, Bsa I, Bst71 I, BsmA I, BsmB I, BsmF I, BspM I, Ear I,Fau I, Fok I, Hga I, Ple I, Sap I, SSfaN I, and Sthi32 I, and morepreferably BceA I and BsmF I.

In one embodiment, the 5′ region of the second primer does not anneal tothe template DNA and/or the 5′ region of the first primer does notanneal to the template DNA. The annealing length of the 3′ region of thefirst or second primer can be 25-20, 20-15, 15, 14, 13, 12, 11, 10, 9,8, 7, 6, 5, 4, or less than 4 bases.

In one embodiment, the amplification can comprise polymerase chainreaction (PCR). In a further embodiment, the annealing temperature forcycle 1 of PCR can be at about the melting temperature of the 3′ regionof the second primer that anneals to the template DNA. In anotherembodiment, the annealing temperature for cycle 2 of PCR can be aboutthe melting temperature of the 3′ region of the first primer thatanneals to the template DNA. In another embodiment, the annealingtemperature for the remaining cycles can be about the meltingtemperature of the entire sequence of the second primer.

In one embodiment, the 3′ end of the second primer is adjacent to thelocus of interest.

The first and/or second primer can contain a tag at the 5′ terminus.

Preferably, the first primer contains a tag at the 5′ terminus. The tagcan be used to separate the amplified DNA from the template DNA. The tagcan be used to separate the amplified DNA containing the labelednucleotide from the amplified DNA that does not contain the labelednucleotide. The tag can be but is not limited to a radioisotope,fluorescent reporter molecule, chemiluminescent reporter molecule,antibody, antibody fragment, hapten, biotin, derivative of biotin,photobiotin, iminobiotin, digoxigenin, avidin, enzyme, acridinium,sugar, enzyme, apoenzyme, homopolymeric oligonucleotide, hormone,ferromagnetic moiety, paramagnetic moiety, diamagnetic moiety,phosphorescent moiety, luminescent moiety, electrochemiluminescentmoiety, chromatic moiety, moiety having a detectable electron spinresonance, electrical capacitance, dielectric constant or electricalconductivity, or combinations thereof. Preferably, the tag is biotin.The biotin tag is used to separate amplified DNA from the template DNAusing a streptavidin matrix. The streptavidin matrix is coated on wellsof a microtiter plate.

The incorporation of a nucleotide in the method of the invention is by aDNA polymerase including but not limited to E. coli DNA polymerase,Klenow fragment of E. coli DNA polymerase I, T5 DNA polymerase, T7 DNApolymerase, T4 DNA polymerase, Taq polymerase, Pfu DNA polymerase, VentDNA polymerase and sequenase.

The incorporation of a nucleotide can further comprise using a mixtureof labeled and unlabeled nucleotides. One nucleotide, two nucleotides,three nucleotides, four nucleotides, five nucleotides, or more than fivenucleotides may be incorporated. A combination of labeled and unlabelednucleotides can be incorporated. The labeled nucleotide can be but isnot limited to a dideoxynucleotide triphosphate and deoxynucleotidetriphosphate. The unlabeled nucleotide can be but is not limited to adideoxynucleotide triphosphate and deoxynucleotide triphosphate. Thelabeled nucleotide is labeled with a molecule such as but not limited toa radioactive molecule, fluorescent molecule, antibody, antibodyfragment, hapten, carbohydrate, biotin, and derivative of biotin,phosphorescent moiety, luminescent moiety, electrochemiluminescentmoiety, chromatic moiety, or moiety having a detectable electron spinresonance, electrical capacitance, dielectric constant or electricalconductivity. Preferably, the labeled nucleotide is labeled with afluorescent molecule. The incorporation of a fluorescent labelednucleotide further includes using a mixture of fluorescent and unlabelednucleotides.

In one embodiment, the determination of the sequence of the locus ofinterest comprises detecting the incorporated nucleotide. In oneembodiment, the detection is by a method such as but not limited to gelelectrophoresis, capillary electrophoresis, microchannelelectrophoresis, polyacrylamide gel electrophoresis, fluorescencedetection, sequencing, ELISA, mass spectrometry, time of flight massspectrometry, quadrupole mass spectrometry, magnetic sector massspectrometry, electric sector mass spectrometry, fluorometry, infraredspectrometry, ultraviolet spectrometry, palentiostatic amperometry,hybridization, such as Southern Blot, or microarray. In a preferredembodiment, the detection is by fluorescence detection.

In a preferred embodiment, the locus of interest is suspected ofcontaining a single nucleotide polymorphism or mutation. The method canbe used for determining sequences of multiple loci of interestconcurrently. The template DNA can comprise multiple loci from a singlechromosome. The template DNA can comprise multiple loci from differentchromosomes. The loci of interest on template DNA can be amplified inone reaction. Alternatively, each of the loci of interest on templateDNA can be amplified in a separate reaction. The amplified DNA can bepooled together prior to digestion of the amplified DNA. Each of thelabeled DNA containing a locus of interest can be separated prior todetermining the sequence of the locus of interest. In one embodiment, atleast one of the loci of interest is suspected of containing a singlenucleotide polymorphism or a mutation.

In another embodiment, the method of the invention can be used fordetermining the sequences of multiple loci of interest from a singleindividual or from multiple individuals. Also, the method of theinvention can be used to determine the sequence of a single locus ofinterest from multiple individuals.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A. A Schematic diagram depicting a double stranded DNA molecule. Apair of primers, depicted as bent arrows, flank the locus of interest,depicted as a triangle symbol at base N14. The locus of interest can bea single nucleotide polymorphism, point mutation, insertion, deletion,translocation, etc. Each primer contains a restriction enzymerecognition site about 10 bp from the 5′ terminus depicted as region “a”in the first primer and as region “d” in the second primer. Restrictionrecognition site “a” can be for any type of restriction enzyme butrecognition site “d” is for a restriction enzyme, which cuts “n”nucleotides away from its recognition site and leaves a 5′ overhang anda recessed 3′ end. Examples of such enzymes include but are not limitedto BceA I and BsmF I. The 5′ overhang serves as a template forincorporation of a nucleotide into the 3′ recessed end.

The first primer is shown modified with biotin at the 5′ end to aid inpurification. The sequence of the 3′ end of the primers is such that theprimers anneal at a desired distance upstream and downstream of thelocus of interest. The second primer anneals close to the locus ofinterest; the annealing site, which is depicted as region “c,” isdesigned such that the 3′ end of the second primer anneals one base awayfrom the locus of interest. The second primer can anneal any distancefrom the locus of interest provided that digestion with the restrictionenzyme, which recognizes the region “d” on this primer, generates a 5′overhang that contains the locus of interest.

The first primer annealing site, which is depicted as region “b,” isabout 20 bases.

FIG. 1B. A schematic diagram depicting the annealing and extension stepsof the first cycle of amplification by PCR. The first cycle ofamplification is performed at about the melting temperature of the 3′region, which anneals to the template DNA, of the second primer,depicted as region “c,” and is 13 base pairs in this example. At thistemperature, both the first and second primers anneal to theirrespective complementary strands and begin extension, depicted by dottedlines. In this first cycle, the second primer extends and copies theregion b where the first primer can anneal in the next cycle.

FIG. 1C. A schematic diagram depicting the annealing and extension stepsfollowing denaturation in the second cycle of amplification of PCR. Thesecond cycle of amplification is performed at a higher annealingtemperature (TM2), which is about the melting temperature of the 20 bpof the 3′ region of the first primer that anneals to the template DNA,depicted as region “b.” Therefore at TM2, the first primer, which iscomplementary to region b, can bind to the DNA that was copied in thefirst cycle of the reaction. However, at TM2 the second primer cannotanneal to the original template DNA or to DNA that was copied in thefirst cycle of the reaction because the annealing temperature is toohigh. The second primer can anneal to 13 bases in the original templateDNA but TM2 is calculated at about the melting temperature of 20 bases.

FIG. 1D. A schematic diagram depicting the annealing and extensionreactions after denaturation during the third cycle of amplification. Inthis cycle, the annealing temperature, TM3, is about the meltingtemperature of the entire second primer, including regions “c” and “d.”The length of regions “c”+“d” is about 27-33 bp long, and thus TM3 issignificantly higher than TM1 and TM2. At this higher TM the secondprimer, which contain region c and d, anneals to the copied DNAgenerated in cycle 2.

FIG. 1E. A schematic diagram depicting the annealing and extensionreactions for the remaining cycles of amplification. The annealingtemperature for the remaining cycles is TM3, which is about the meltingtemperature of the entire second primer. At TM3, the second primer bindsto templates that contain regions c′ and d′ and the first primer bindsto templates that contain regions a′ and b. By raising the annealingtemperature successively in each cycle for the first three cycles, fromTM1 to TM2 to TM3, nonspecific amplification is significantly reduced.

FIG. 1F. A schematic diagram depicting the amplified locus of interestbound to a solid matrix.

FIG. 1G. A schematic diagram depicting the bound, amplified DNA afterdigestion with a restriction enzyme that recognizes “d.” The“downstream” end is released into the supernatant, and can be removed bywashing with any suitable buffer. The upstream end containing the locusof interest remains bound to the solid matrix.

FIG. 1H. A schematic diagram depicting the bound amplified DNA, after“filling in” with a labeled ddNTP. A DNA polymerase is used to “fill in”the base (N′₁₄) that is complementary to the locus of interest (N₁₄). Inthis example, only ddNTPs are present in this reaction, such that onlythe locus of interest or SNP of interest is filled in.

FIG. 1I. A schematic diagram depicting the labeled, bound DNA afterdigestion with restriction enzyme “a.” The labeled DNA is released intothe supernatant, which can be collected to identify the base that wasincorporated.

FIG. 2. A schematic diagram depicting double stranded DNA templates with“N” number of loci of interest and “n” number of primer pairs, x₁, y₁,to x_(n), y_(n), specifically annealed such that a primer flanks eachlocus of interest. The first primers are biotinylated at the 5′ end,depicted by ●, and contain a restriction enzyme recognition site, “a”,which is recognized by any type of restriction enzyme. The secondprimers contain a restriction enzyme recognition site, “d,” where “d” isa recognition site for a restriction enzyme that cuts DNA at a distancefrom its recognition site, and generates a 5′ overhang containing thelocus of interest and a recessed 3′ end. The second primers annealadjacent to the respective loci of interest. The exact position of therestriction enzyme site “d” in the second primers is designed such thatdigesting the PCR product of each locus of interest with restrictionenzyme “d” generates a 5′ overhang containing the locus of interest anda 3′ recessed end. The annealing sites of the first primers are about 20bases long and are selected such that each successive first primer isfurther away from its respective second primer. For example, if at locus1 the 3′ ends of the first and second primers are Z base pairs apart,then at locus 2, the 3′ ends of the first and second primers are Z+Kbase pairs apart, where K=1, 2, 3 or more than three bases. Primers forlocus N are Z_(N-1)+K base pairs apart. The purpose of making eachsuccessive first primer further apart from their respective secondprimers is such that the “filled in” restriction fragments (generatedafter amplification, purification, digestion and labeling as describedin FIGS. 1B-1I) differ in size and can be resolved, for example byelectrophoresis, to allow detection of each individual locus ofinterest.

FIG. 3. PCR amplification of SNPs using multiple annealing temperatures.A sample containing genomic DNA templates from thirty-six humanvolunteers was analyzed for the following four SNPs: SNP HC21S00340(lane 1), identification number as assigned in the Human Chromosome 21cSNP Database, located on chromosome 21; SNP TSC 0095512 (lane 2),located on chromosome 1; SNP TSC 0214366 (lane 3), located on chromosome1; and SNP TSC 0087315 (lane 4), located on chromosome 1. Each SNP wasamplified by PCR using three different annealing temperature protocols,herein referred to as the low stringency annealing temperature; mediumstringency annealing temperature; and high stringency annealingtemperature. Regardless of the annealing temperature protocol, each SNPwas amplified for 40 cycles of PCR. The denaturation step for each PCRreaction was performed for 30 seconds at 95° C.

FIG. 3A. Photograph of a gel demonstrating PCR amplification of the 4different SNPs using the low stringency annealing temperature protocol.

FIG. 3B. Photograph of a gel demonstrating PCR amplification of the 4different SNPs using the medium stringency annealing temperatureprotocol.

FIG. 3C. Photograph of a gel demonstrating PCR amplification of the 4different SNPs using the high stringency annealing temperature protocol.

FIG. 4A. A depiction of the DNA sequence of SNP HC21S00027 (SEQ IDNOS:27 & 28), assigned by the Human Chromosome 21 cSNP database, locatedon chromosome 21. A first primer (SEQ ID NO:17) and a second primer (SEQID NO:18) are indicated above and below, respectively, the sequence ofHC21S00027. The first primer is biotinylated and contains therestriction enzyme recognition site for EcoRI. The second primercontains the restriction enzyme recognition site for BsmF I and contains13 bases that anneal to the DNA sequence. The SNP is indicated by R(A/G) and r (T/C; complementary to R).

FIG. 4B. A depiction of the DNA sequence of SNP HC21S00027 (SEQ IDNOS:27 & 28), as assigned by the Human Chromosome 21 cSNP database,located on chromosome 21. A first primer (SEQ ID NO:17) and a secondprimer (SEQ ID NO:19) are indicated above and below, respectively, thesequence of HC21S00027. The first primer is biotinylated and containsthe restriction enzyme recognition site for EcoRI. The second primercontains the restriction enzyme recognition site for BceA I and has 13bases that anneal to the DNA sequence. The SNP is indicated by R (A/G)and r (T/C; complementary to R).

FIG. 4C. A depiction of the DNA sequence of SNP TSC0095512 (SEQ IDNOS:29 & 30) from chromosome 1. The first primer (SEQ ID NO:11) and thesecond primer (SEQ ID NO:20) are indicated above and below,respectively, the sequence of TSC0095512. The first primer isbiotinylated and contains the restriction enzyme recognition site forEcoRI. The second primer contains the restriction enzyme recognitionsite for BsmF I and has 13 bases that anneal to the DNA sequence. TheSNP is indicated by S (G/C) and s (C/G; complementary to S).

FIG. 4D. A depiction of the DNA sequence of SNP TSC0095512 (SEQ IDNOS:29 & 30) from chromosome 1. The first primer (SEQ ID NO:11) and thesecond primer (SEQ ID NO:12) are indicated above and below,respectively, the sequence of TSC0095512. The first primer isbiotinylated and contains the restriction enzyme recognition site forEcoRI. The second primer contains the restriction enzyme recognitionsite for BceA I and has 13 bases that anneal to the DNA sequence. TheSNP is indicated by S (G/C) and s (C/G; complementary to S).

FIGS. 5A-5D. A schematic diagram depicting the nucleotide sequences ofSNP HC21S00027 (FIG. 5A (SEQ ID NOS:31 & 32) and FIG. 5B (SEQ ID NOS:31& 33)), and SNP TSC0095512 (FIG. 5C (SEQ ID NOS:34 & 35) and FIG. 5D(SEQ ID NOS:34 & 36)) after amplification with the primers described inFIGS. 4A-4D. Restriction sites in the primer sequence are indicated inbold.

FIGS. 6A-6D. A schematic diagram depicting the nucleotide sequences ofeach amplified SNP after digestion with the appropriate Type IISrestriction enzyme. FIG. 6A (SEQ ID NOS:31 & 32) and FIG. 6B (SEQ IDNOS:31 & 33) depict fragments of SNP HC21S00027 digested with the TypeIIS restriction enzymes BsmF I and BceA I, respectively. FIG. 6C (SEQ IDNOS:34 & 35) and FIG. 6D (SEQ ID NOS:34 & 36) depict fragments of SNPTSC0095512 digested with the Type IIS restriction enzymes BsmF I andBceA I, respectively.

FIGS. 7A-7D. A schematic diagram depicting the incorporation of afluorescently labeled nucleotide using the 5′ overhang of the digestedSNP site as a template to “fill in” the 3′ recessed end. FIG. 7A (SEQ IDNOS:31, 37 & 41) and FIG. 7B (SEQ ID NOS:31, 37 & 39) depict thedigested SNP HC21S00027 locus with an incorporated labeled ddNTP(*R^(−dd)=fluorescent dideoxy nucleotide). FIG. 7C (SEQ ID NOS:34 & 38)and FIG. 7D (SEQ ID NO:34) depict the digested SNP TSC0095512 locus withan incorporated labeled ddNTP (*S^(−dd)=fluorescent dideoxy nucleotide).The use of ddNTPs ensures that the 3′ recessed end is extended by onenucleotide, which is complementary to the nucleotide of interest or SNPsite present in the 5′ overhang.

FIG. 7E. A schematic diagram depicting the incorporation of dNTPs and addNTP into the 5′ overhang containing the SNP site. SNP HC21S00007 wasdigested with BsmF I, which generates a four base 5′ overhang. The useof a mixture of dNTPs and ddNTPs allows the 3′ recessed end to beextended one nucleotide (a ddNTP is incorporated first) (SEQ ID NOS:31,37 & 41); two nucleotides (a dNTP is incorporated followed by a ddNTP)(SEQ ID NOS:31, 39 & 41); three nucleotides (two dNTPs are incorporated,followed by a ddNTP) (SEQ ID NOS:31, 40 & 41); or four nucleotides(three dNTPs are incorporated, followed by a ddNTP) (SEQ ID NOS:31 &41). All four products can be separated by size, and the incorporatednucleotide detected (*R^(−dd)=fluorescent dideoxy nucleotide). Detectionof the first nucleotide, which corresponds to the SNP or locus site, andthe next three nucleotides provides an additional level of qualityassurance. The SNP is indicated by R (A/G) and r (T/C) (complementary toR).

FIGS. 8A-8D. Release of the “filled in” SNP from the solid supportmatrix, i.e. streptavidin coated well. SNP HC21S00027 is shown in FIG.8A (SEQ ID NOS:31, 37 & 41) and FIG. 8B (SEQ ID NOS:31, 37 & 39), whileSNP TSC0095512 is shown in FIG. 8C (SEQ ID NOS:34 & 38) and FIG. 8D (SEQID NO:34). The “filled in” SNP is free in solution, and can be detected.

FIG. 9A. Sequence analysis of SNP HC21S00027 digested with BceAI. Four“fill in” reactions are shown; each reaction contained one fluorescentlylabeled nucleotide, ddGTP, ddATP, ddTTP, or ddCTP, and unlabeled ddNTPs.The 5′ overhang generated by digestion with BceA I and the expectednucleotides at this SNP site are indicated.

FIG. 9B. Sequence analysis of SNP TSC0095512. SNP TSC0095512 wasamplified with a second primer that contained the recognition site forBceA I, and in a separate reaction, with a second primer that containedthe recognition site for BsmF I. Four fill in reactions are shown foreach PCR product; each reaction contained one fluorescently labelednucleotide, ddGTP, ddATP, ddTTP, or ddCTP, and unlabeled ddNTPs. The 5′overhang generated by digestion with BceA I and with BsmF I and theexpected nucleotides are indicated.

FIG. 9C. Sequence analysis of SNP TSC0264580 after amplification with asecond primer that contained the recognition site for BsmF I. Four “fillin” reactions are shown; each reaction contained one fluorescentlylabeled nucleotide, which was ddGTP, ddATP, ddTTP, or ddCTP andunlabeled ddNTPs. Two different 5′ overhangs are depicted: onerepresents the DNA molecules that were cut 11 nucleotides away on thesense strand and 15 nucleotides away on the antisense strand and theother represents the DNA molecules that were cut 10 nucleotides away onthe sense strand and 14 nucleotides away on the antisense strand. Theexpected nucleotides also are indicated.

FIG. 9D. Sequence analysis of SNP HC21S00027 amplified with a secondprimer that contained the recognition site for BsmF I. A mixture oflabeled ddNTPs and unlabeled dNTPs was used to fill in the 5′ overhanggenerated by digestion with BsmF I. Two different 5′ overhangs aredepicted: one represents the DNA molecules that were cut 11 nucleotidesaway on the sense strand and 15 nucleotides away on the antisense strandand the other represents the DNA molecules that were cut 10 nucleotidesaway on the sense strand and 14 nucleotides away on the antisensestrand. The nucleotide upstream of the SNP, the nucleotide at the SNPsite (the sample contained DNA templates from 36 individuals; bothnucleotides would be expected to be represented in the sample), and thethree nucleotides downstream of the SNP are indicated.

FIG. 10. Sequence analysis of multiple SNPs. SNPs HC21S00131, andHC21S00027, which are located on chromosome 21, and SNPs TSC0087315, SNPTSC0214366, SNP TSC0413944, and SNP TSC0095512, which are on chromosome1, were amplified in separate PCR reactions with second primers thatcontained a recognition site for BsmF I. The primers were designed sothat each amplified locus of interest was of a different size. Afteramplification, the reactions were pooled into a single sample, and allsubsequent steps of the method performed (as described for FIGS. 1F-1I)on that sample. Each SNP and the nucleotide found at each SNP areindicated.

DETAILED DESCRIPTION OF THE INVENTION

The present invention provides a novel method for rapidly determiningthe sequence of DNA, especially at a locus of interest or multiple lociof interest. The sequences of any number of DNA targets, from one tohundreds or thousands or more of loci of interest in any template DNA orsample of nucleic acid can be determined efficiently, accurately, andeconomically. The method is especially useful for the rapid sequencingof one to tens of thousands or more of genes, regions of genes,fragments of genes, single nucleotide polymorphisms, and mutations on asingle chromosome or on multiple chromosomes.

The invention is directed to a method for determining a sequence of alocus of interest, the method comprising: (a) amplifying a locus ofinterest on a template DNA using a first and second primers, wherein thesecond primer contains a recognition site for a restriction enzyme suchthat digestion with the restriction enzyme generates a 5′ overhangcontaining the locus of interest; (b) digesting the amplified DNA withthe restriction enzyme that recognizes the recognition site on thesecond primer; (c) incorporating a nucleotide into the digested DNA of(b) by using the 5′ overhang containing the locus of interest as atemplate; and (d) determining the sequence of the locus of interest bydetermining the sequence of the DNA of (c).

The invention is also directed to a method for determining a sequence ofa locus of interest, said method comprising: (a) amplifying a locus ofinterest on a template DNA using a first and second primers, wherein thefirst and/or second primer contains a portion of a recognition site fora restriction enzyme, wherein a full recognition site for therestriction enzyme is generated upon amplification of the template DNAsuch that digestion with the restriction enzyme generates a 5′ overhangcontaining the locus of interest; (b) digesting the amplified DNA withthe restriction enzyme that recognizes the full recognition sitegenerated by the second primer and the template DNA; (c) incorporating anucleotide into the digested DNA of (b) by using the 5′ overhangcontaining the locus of interest as a template; and determining thesequence of the locus of interest by determining the sequence of the DNAof (c).

DNA Template

By a “locus of interest” is intended a selected region of nucleic acidthat is within a larger region of nucleic acid. A locus of interest caninclude but is not limited to 1-100, 1-50, 1-20, or 1-10 nucleotides,preferably 1-6, 1-5, 1-4, 1-3, 1-2, or 1 nucleotide(s).

The term “template” refers to any nucleic acid molecule that can be usedfor amplification in the invention. RNA or DNA that is not naturallydouble stranded can be made into double stranded DNA so as to be used astemplate DNA. Any double stranded DNA or preparation containingmultiple, different double stranded DNA molecules can be used astemplate DNA to amplify a locus or loci of interest contained in thetemplate DNA.

The source of the nucleic acid for obtaining the template DNA can befrom any appropriate source including but not limited to nucleic acidfrom any organism, e.g., human or nonhuman, e.g., bacterium, virus,yeast, fungus, plant, protozoan, animal, nucleic acid-containing samplesof tissues, bodily fluids (for example, blood, serum, plasma, saliva,urine, tears, semen, vaginal secretions, lymph fluid, cerebrospinalfluid or mucosa secretions), fecal matter, individual cells or extractsof the such sources that contain the nucleic acid of the same, andsubcellular structures such as mitochondria or chloroplasts, usingprotocols well established within the art. Nucleic acid can also beobtained from forensic, food, archaeological, or inorganic samples ontowhich nucleic acid has been deposited or extracted. In a preferredembodiment, the nucleic acid has been obtained from a human or animal tobe screened for the presence of one or more genetic sequences that canbe diagnostic for, or predispose the subject to, a medical condition ordisease.

The nucleic acid that is to be analyzed can be any nucleic acid, e.g.,genomic, plasmid, cosmid, yeast artificial chromosomes, artificial orman-made DNA, including unique DNA sequences, and also DNA that has beenreverse transcribed from an RNA sample, such as cDNA. The sequence ofRNA can be determined according to the invention if it is capable ofbeing made into a double stranded DNA form to be used as template DNA.

The terms “primer” and “oligonucleotide primer” are interchangeable whenused to discuss an oligonucleotide that anneals to a template and can beused to prime the synthesis of a copy of that template.

“Amplified” DNA is DNA that has been “copied” once or multiple times,e.g. by polymerase chain reaction. When a large amount of DNA isavailable to assay, such that a sufficient number of copies of the locusof interest are already present in the sample to be assayed, it may notbe necessary to “amplify” the DNA of the locus of interest into an evenlarger number of replicate copies. Rather, simply “copying” the templateDNA once using a set of appropriate primers, such as those containinghairpin structures that allow the restriction enzyme recognition sitesto be double stranded, can suffice.

“Copy” as in “copied DNA” refers to DNA that has been copied once, orDNA that has been amplified into more than one copy.

In one embodiment, the nucleic acid is amplified directly in theoriginal sample containing the source of nucleic acid. It is notessential that the nucleic acid be extracted, purified or isolated; itonly needs to be provided in a form that is capable of being amplified.A hybridization step of the nucleic acid with the primers, prior toamplification, is not required. For example, amplification can beperformed in a cell or sample lysate using standard protocols well knownin the art. DNA that is on a solid support, in a fixed biologicalpreparation, or otherwise in a composition that contains non-DNAsubstances and that can be amplified without first being extracted fromthe solid support or fixed preparation or non-DNA substances in thecomposition can be used directly, without further purification, as longas the DNA can anneal with appropriate primers, and be copied,especially amplified, and the copied or amplified products can berecovered and utilized as described herein.

In a preferred embodiment, the nucleic acid is extracted, purified orisolated from non-nucleic acid materials that are in the original sampleusing methods known in the art prior to amplification.

In another embodiment, the nucleic acid is extracted, purified orisolated from the original sample containing the source of nucleic acidand prior to amplification, the nucleic acid is fragmented using anynumber of methods well known in the art including but not limited toenzymatic digestion, manual shearing, and sonication. For example, theDNA can be digested with one or more restriction enzymes that have arecognition site, and especially an eight base or six base pairrecognition site, which is not present in the loci of interest.Typically, DNA can be fragmented to any desired length, including 50,100, 250, 500, 1,000, 5,000, 10,000, 50,000 and 100,000 base pairs long.In another embodiment, the DNA is fragmented to an average length ofabout 1000 to 2000 base pairs. However, it is not necessary that the DNAbe fragmented.

Fragments of DNA that contain the loci of interest can be purified fromthe fragments of DNA that do not contain the loci of interest beforeamplification. The purification can be done by using primers that willbe used in the amplification (see “Primer Design” section below) ashooks to retrieve the fragments containing the loci of interest, basedon the ability of such primers to anneal to the loci of interest. In apreferred embodiment, tag-modified primers are used, such as e.g.biotinylated primers. See also the “Purification of Amplified DNA”section for additional tags.

By purifying the DNA fragments containing the loci of interest, thespecificity of the amplification reaction can be improved. This willminimize amplification of nonspecific regions of the template DNA.Purification of the DNA fragments can also allow multiplex PCR(Polymerase Chain Reaction) or amplification of multiple loci ofinterest with improved specificity.

In one embodiment, the nucleic acid sample is obtained with a desiredpurpose in mind such as to determine the sequence at a predeterminedlocus or loci of interest using the method of the invention. Forexample, the nucleic acid is obtained for the purpose of identifying oneor more conditions or diseases to which the subject can be predisposedor is in need of treatment for, or the presence of certain singlenucleotide polymorphisms. In an alternative embodiment, the sample isobtained to screen for the presence or absence of one or more DNAsequence markers, the presence of which would identify that DNA as beingfrom a specific bacterial or fungal microorganism, or individual.

The loci of interest that are to be sequenced can be selected based uponsequence alone. In humans, over 1.42 million single nucleotidepolymorphisms (SNPs) have been described (Nature 409:928-933 (2001); TheSNP Consortium LTD). On the average, there is one SNP every 1.9 kb ofhuman genome. However, the distance between loci of interest need not beconsidered when selecting the loci of interest to be sequenced accordingto the invention. If more than one locus of interest on genomic DNA isbeing analyzed, the selected loci of interest can be on the samechromosome or on different chromosomes.

In a preferred embodiment, the length of sequence that is amplified ispreferably different for each locus of interest so that the loci ofinterest can be separated by size.

In fact, it is an advantage of the invention that primers that copy anentire gene sequence need not be utilized. Rather, the copied locus ofinterest is preferably only a small part of the total gene. There is noadvantage to sequencing the entire gene as this can increase cost anddelay results. Sequencing only the desired bases or loci of interestwithin the gene maximizes the overall efficiency of the method becauseit allows for the maximum number of loci of interest to be determined inthe fastest amount of time and with minimal cost.

Because a large number of sequences can be analyzed together, the methodof the invention is especially amenable to the large-scale screening ofa number of individual samples.

Any number of loci of interest can be analyzed and processed, especiallyconcurrently, using the method of the invention. The sample(s) can beanalyzed to determine the sequence at one locus of interest or atmultiple loci of interest concurrently. For example, the 10 or 20 mostfrequently occurring mutation sites in a disease associated gene can besequenced to detect the majority of the disease carriers.

Alternatively, 2, 3, 4, 5, 6, 7, 8, 9, 10-20, 20-25, 25-30, 30-35,35-40, 40-45, 45-50, 50-100, 100-250, 250-500, 500-1,000, 1,000-2,000,2,000-3,000, 3,000-5,000, 5,000-10,000, 10,000-50,000 or more than50,000 loci of interest can be analyzed at the same time when a globalgenetic screening is desired. Such a global genetic screening might bedesired when using the method of the invention to provide a geneticfingerprint to identify a certain microorganism or individual or for SNPgenotyping.

The multiple loci of interest can be targets from different organisms.For example, a plant, animal or human subject in need of treatment canhave symptoms of infection by one or more pathogens. A nucleic acidsample taken from such a plant, animal or human subject can be analyzedfor the presence of multiple suspected or possible pathogens at the sametime by determining the sequence of loci of interest which, if present,would be diagnostic for that pathogen. Not only would the finding ofsuch a diagnostic sequence in the subject rapidly pinpoint the cause ofthe condition, but also it would rule out other pathogens that were notdetected. Such screening can be used to assess the degree to which apathogen has spread throughout an organism or environment. In a similarmanner, nucleic acid from an individual suspected of having a diseasethat is the result of a genetic abnormality can be analyzed for some orall of the known mutations that result in the disease, or one or more ofthe more common mutations.

The method of the invention can be used to monitor the integrity of thegenetic nature of an organism. For example, samples of yeast can betaken at various times and from various batches in the brewing process,and their presence or identity compared to that of a desired strain bythe rapid analysis of their genomic sequences as provided herein.

The locus of interest that is to be copied can be within a codingsequence or outside of a coding sequence. Preferably, one or more lociof interest that are to be copied are within a gene. In a preferredembodiment, the template DNA that is copied is a locus or loci ofinterest that is within a genomic coding sequence, either intron orexon. In a highly preferred embodiment, exon DNA sequences are copied.The loci of interest can be sites where mutations are known to causedisease or predispose to a disease state. The loci of interest can besites of single nucleotide polymorphisms. Alternatively, the loci ofinterest that are to be copied can be outside of the coding sequence,for example, in a transcriptional regulatory region, and especially apromoter, enhancer, or repressor sequence.

Primer Design

Published sequences, including consensus sequences, can be used todesign or select primers for use in amplification of template DNA. Theselection of sequences to be used for the construction of primers thatflank a locus of interest can be made by examination of the sequence ofthe loci of interest, or immediately thereto. The recently publishedsequence of the human genome provides a source of useful consensussequence information from which to design primers to flank a desiredhuman gene locus of interest.

By “flanking” a locus of interest is meant that the sequences of theprimers are such that at least a portion of the 3′ region of one primeris complementary to the antisense strand of the template DNA andupstream of the locus of interest (forward primer), and at least aportion of the 3′ region of the other primer is complementary to thesense strand of the template DNA and downstream of the locus of interest(reverse primer). A “primer pair” is intended to specify a pair offorward and reverse primers. Both primers of a primer pair anneal in amanner that allows extension of the primers, such that the extensionresults in amplifying the template DNA in the region of the locus ofinterest.

Primers can be prepared by a variety of methods including but notlimited to cloning of appropriate sequences and direct chemicalsynthesis using methods well known in the art (Narang et al., MethodsEnzymol. 68:90 (1979); Brown et al., Methods Enzymol. 68:109 (1979)).Primers can also be obtained from commercial sources such as OperonTechnologies, Amersham Pharmacia Biotech, Sigma, and Life Technologies.The primers of a primer pair can have the same length. Alternatively,one of the primers of the primer pair can be longer than the otherprimer of the primer pair. The primers can have an identical meltingtemperature. The lengths of the primers can be extended or shortened atthe 5′ end or the 3′ end to produce primers with desired meltingtemperatures. In a preferred embodiment, the 3′ annealing lengths of theprimers, within a primer pair, differ. Also, the annealing position ofeach primer pair can be designed such that the sequence and length ofthe primer pairs yield the desired melting temperature. The simplestequation for determining the melting temperature of primers smaller than25 base pairs is the Wallace Rule (Td=2(Λ+T)+4(G+C)). Computer programscan also be used to design primers, including but not limited to ArrayDesigner Software (Arrayit Inc.), Oligonucleotide Probe Sequence DesignSoftware for Genetic Analysis (Olympus Optical Co.), NetPrimer, andDNAsis from Hitachi Software Engineering. The TM (melting or annealingtemperature) of each primer is calculated using software programs suchas Net Primer (free web based program at available at world wide web:premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html. (internetaddress as of Feb. 13, 2002).

In another embodiment, the annealing temperature of the primers can berecalculated and increased after any cycle of amplification, includingbut not limited to cycle 1, 2, 3, 4, 5, cycles 6-10, cycles 10-15,cycles 15-20, cycles 20-25, cycles 25-30, cycles 30-35, or cycles 35-40.After the initial cycles of amplification, the 5′ half of the primers isincorporated into the products from each loci of interest, thus the TMcan be recalculated based on both the sequences of the 5′ half and the3′ half of each primer.

For example, in FIG. 1B, the first cycle of amplification is performedat about the melting temperature of the 3′ region of the second primer(region “c”) that anneals to the template DNA, which is 13 bases. Afterthe first cycle, the annealing temperature can be raised to TM2, whichis about the melting temperature of the 3′ region of the first primer(region “b′”) that anneals to the template DNA. The second primer cannotbind to the original template DNA because it only anneals to 13 bases inthe original DNA template, and TM2 is about the melting temperature ofapproximately 20 bases, which is the 3′ annealing region of the firstprimer (FIG. 1C). However, the first primer can bind to the DNA that wascopied in the first cycle of the reaction. In the third cycle, theannealing temperature is raised to TM3, which is about the meltingtemperature of the entire sequence of the second primer (“c” and “d”).The template DNA produced from the second cycle of PCR contains bothregions c′ and d′, and therefore, the second primer can anneal andextend at TM3 (FIG. 1D). The remaining cycles are performed at TM3. Theentire sequence of the first primer (a+b′) can anneal to the templatefrom the third cycle of PCR, and extend (FIG. 1E). Increasing theannealing temperature will decrease non-specific binding and increasethe specificity of the reaction, which is especially useful ifamplifying a locus of interest from human genomic DNA, which contains3×10⁹ base pairs.

As used herein, the term “about” with regard to annealing temperaturesis used to encompass temperatures within 10 degrees Celsius of thestated temperatures.

In one embodiment, one primer pair is used for each locus of interest.However, multiple primer pairs can be used for each locus of interest.

In one embodiment, primers are designed such that one or both primers ofthe primer pair contain sequence in the 5′ region for one or morerestriction endonucleases (restriction enzyme).

As used herein, with regard to the position at which restriction enzymesdigest DNA, the “sense” strand is the strand reading 5′ to 3′ in thedirection in which the restriction enzyme cuts. For example, BsmF Irecognizes the following sequence:

5′  GGGAC(N)₁₀↓ 3′ (SEQ ID NO:1) 3′  CCCTG(N)₁₄↑  5′ or 5′↓ (N)₁₄GTCCC3′ (SEQ ID NO:2) 3′↑ (N)₁₀CAGGG 5′

Thus, the sense strand is the strand containing the “GGGAC” sequence asit reads 5′ to 3′ in the direction that the restriction enzyme cuts.

As used herein, with regard to the position at which restriction enzymesdigest DNA, the “antisense” strand is the strand reading 3′ to 5′ in thedirection in which the restriction enzyme cuts. Thus, the antisensestrand is the strand that contains the “ccctg” sequence as it reads 3′to 5′.

In the invention, one of the primers in a primer pair can be designedsuch that it contains a restriction enzyme recognition site for arestriction enzyme such that digestion with the restriction enzymeproduces a recessed 3′ end and a 5′ overhang that contains the locus ofinterest (herein referred to as a “second primer”). For example, thesecond primer of a primer pair can contain a recognition site for arestriction enzyme that does not cut DNA at the recognition site butcuts “n” nucleotides away from the recognition site. “N” is a distancefrom the recognition site to the site of the cut by the restrictionenzyme. If the recognition sequence is for the restriction enzyme BceAI, the enzyme will cut ten (10) nucleotides from the recognition site onthe sense strand, and twelve (12) nucleotides away from the recognitionsite on the antisense strand.

The 3′ region and preferably the 3′ half of the primers is designed toanneal to a sequence that flanks the loci of interest (FIG. 1A). Thesecond primer may anneal any distance from the locus of interestprovided that digestion with the restriction enzyme that recognizes therestriction enzyme recognition site on this primer generates a 5′overhang that contains the locus of interest. The 5′ overhang can be ofany size, including but not limited to 1, 2, 3, 4, 5, 6, 7, 8, and morethan 8 bases.

In a preferred embodiment, the 3′ end of the second primer can anneal 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or more than 14 bases fromthe locus of interest or at the locus of interest.

In a preferred embodiment, the second primer is designed to annealcloser to the locus of interest than the other primer of a primer pair(the other primer is herein referred to as a “first primer”). The secondprimer can be a forward or reverse primer and the first primer can be areverse or forward primer, respectively. Whether the first or secondprimer should be the forward or reverse primer can be determined bywhich design will provide better sequencing results.

For example, the primer that anneals closer to the locus of interest cancontain a recognition site for the restriction enzyme BsmF I, which cutsten (10) nucleotides from the recognition site on the sense strand, andfourteen (14) nucleotides from the recognition site on the antisensestrand. In this case, the primer can be designed so that the restrictionenzyme recognition site is 13 bases, 12 bases, 10 bases or 11 bases fromthe locus of interest. If the recognition site is 13 bases from thelocus of interest, digestion with BsmF I will generate a 5′ overhang(RXXX), wherein the locus of interest (R) is the first nucleotide in theoverhang (reading 3′ to 5′), and X is any nucleotide. If the recognitionsite is 12 bases from the locus of interest, digestion with BsmF I willgenerate a 5′ overhang (XRXX), wherein the locus of interest (R) is thesecond nucleotide in the overhang (reading 3′ to 5′). If the recognitionsite is 11 bases from the locus of interest, digestion with BsmF I willgenerate a 5′ overhang (XXRX), wherein the locus of interest (R) is thethird nucleotide in the overhang (reading 3′ to 5′). The distancebetween the restriction enzyme recognition site and the locus ofinterest should be designed so that digestion with the restrictionenzyme generates a 5′ overhang, which contains the locus of interest.The effective distance between the recognition site and the locus ofinterest will vary depending on the choice of restriction enzyme.

In another embodiment, the second primer, which can anneal closer to thelocus of interest relative to the first primer, can be designed so thatthe restriction enzyme that generates the 5′ overhang, which containsthe locus of interest, will see the same sequence at the cut site,independent of the nucleotide at the locus of interest. For example, ifthe primer that anneals closer to the locus of interest is designed sothat the recognition site for the restriction enzyme BsmF I (5′ GGGAC3′) is thirteen bases from the locus of interest, the restriction enzymewill cut the antisense strand one base upstream of the locus ofinterest. The nucleotide at the locus of interest is adjacent to the cutsite, and may vary from DNA molecule to DNA molecule. If it is desiredthat the nucleotides adjacent to the cut site be identical, the primercan be designed so that the restriction enzyme recognition site for BsmFI is twelve bases away from the locus of interest. Digestion with BsmF Iwill generate a 5′ overhang, wherein the locus of interest is in thesecond position of the overhang (reading 3′ to 5′) and is no longeradjacent to the cut site. Designing the primer so that the restrictionenzyme recognition site is twelve (12) bases from the locus of interestallows the nucleotides adjacent to the cut site to be the same,independent of the nucleotide at the locus of interest. Also, primersthat have been designed so that the restriction enzyme recognition siteis eleven (11) or ten (10) bases from the locus of interest will allowthe nucleotides adjacent to the cut site to be the same, independent ofthe nucleotide at the locus of interest.

The 3′ end of the first primer (either the forward or the reverse) canbe designed to anneal at a chosen distance from the locus of interest.Preferably, for example, this distance is between 10-25, 25-50, 50-75,75-100, 100-150, 150-200, 200-250, 250-300, 300-350, 350-400, 400-450,450-500, 500-550, 550-600, 600-650, 650-700, 700-750, 750-800, 800-850,850-900, 900-950, 950-1000 and greater than 1000 bases away from thelocus of interest. The annealing sites of the first primers are chosensuch that each successive upstream primer is further and further awayfrom its respective downstream primer.

For example, if at locus of interest 1 the 3′ ends of the first andsecond primers are Z bases apart, then at locus of interest 2, the 3′ends of the upstream and downstream primers are Z+K bases apart, whereK=1, 2, 3, 4, 5-10, 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80,80-90, 90-100, 100-200, 200-300, 300-400, 400-500, 500-600, 600-700,700-800, 800-900, 900-1000, or greater than 1000 bases (FIG. 2). Thepurpose of making the upstream primers further and further apart fromtheir respective downstream primers is so that the PCR products of allthe loci of interest differ in size and can be separated, e.g., on asequencing gel. This allows for multiplexing by pooling the PCR productsin later steps.

In one embodiment, the 5′ region of the first primer can have arecognition site for any type of restriction enzyme. In a preferredembodiment, the first primer has at least one restriction enzymerecognition site that is different from the restriction enzymerecognition site in the second primer. In another preferred embodiment,the first primer anneals further away from the locus of interest thanthe second primer.

In a preferred embodiment, the second primer contains a restrictionenzyme recognition sequence for a Type IIS restriction enzyme includingbut not limited to BceA I and BsmF I, which produce a two base 5′overhang and a four base 5′ overhang, respectively. Restriction enzymesthat are Type IIS are preferred because they recognize asymmetric basesequences (not palindromic like the orthodox Type II enzymes). Type IISrestriction enzymes cleave DNA at a specified position that is outsideof the recognition site, typically up to 20 base pairs outside of therecognition site. These properties make Type IIS restriction enzymes,and the recognition sites thereof, especially useful in the method ofthe invention. Preferably, the Type IIS restriction enzymes used in thismethod leave a 5′ overhang and a recessed 3′ end.

A wide variety of Type IIS restriction enzymes are known and suchenzymes have been isolated from bacteria, phage, archeabacteria andviruses of eukaryotic algae and are commercially available (Promega,Madison Wis.; New England Biolabs, Beverly, Mass.; Szybalski W. et al.,Gene 100:13-16, (1991)). Examples of Type IIS restriction enzymes thatwould be useful in the method of the invention include, but are notlimited to enzymes such as those listed in Table I.

TABLE I Type IIS restriction enzymes that generate a 5′  overhang and arecessed 3′  end. Enzyme-Source Recognition/Cleavage Site Supplier AlwI-Acinetobacter lwoffii GGATC(4/5) NE Biolabs Alw26 I-Acinetobacterlwoffi GTCTC(1/5) Promega Bbs I-Bacillus laterosporus GAAGAC(2/6) NEBiolabs Bbv I-Bacillus brevis GCAGC(8/12) NE Biolabs BceA I-Bacilluscereus 1315 ACGGC(12/14) NE Biolabs Bmr I-Bacillus megateriumACTGGG(5/4) NE Biolabs Bsa I-Bacillus stearothermophilus 6-55GGTCTC(1/5) NE Biolabs Bst71 I-Bacillus stearothermophilus 71GCAGC(8/12) Promega BsmA I-Bacillus stearothermophilus A664 GTCTC(1/5)NE Biolabs BsmB I-Bacillus stearotherinophilus B61 CGTCTC(1/5) NEBiolabs BsmF I-Bacillus stearothermophilus F GGGAC(1O/14) NE BiolabsBspM I-Bacillus species M ACCTGC(4/8) NE Biolabs Ear I-Enterobacteraerogenes CTCTTC(1/4) NE Biolabs Fau I-Flavobacterium aquatileCCCGC(416) NE Biolabs Fok I-Flavobacterium okeonokoites GGATG(9/13) NEBiolabs Hga I-Haemophilus gallinarum GACGC(5/10) NE Biolabs PleI-Pseudomonas lemoignei GAGTC(4/5) NE Biolabs Sap I-Saccharopolysporaspecies GCTCTTC(1/4) NE Biolabs SfaN I-Streptococcus faecalis ND547GCATC(5/9) NE Biolabs Sth 132 I-Streptococcus thermophilus CCCG(4/8) Nocommercial ST132 supplier (Gene 195:201-206 (1997))

In one embodiment, a primer pair has sequence at the 5′ region of eachof the primers that provides a restriction enzyme recognition site thatis unique for one restriction enzyme.

In another embodiment, a primer pair has sequence at the 5′ region ofeach of the primers that provide a restriction site that is recognizedby more than one restriction enzyme, and especially for more than oneType IIS restriction enzyme. For example, certain consensus sequencescan be recognized by more than one enzyme. For example, BsgI, Eco57I andBpmI all recognize the consensus 5′ (G/C)TgnAG 3′ and cleave 16 bp awayon the antisense strand and 14 bp away on the sense strand. A primerthat provides such a consensus sequence would result in a product thathas a site that can be recognized by any of the restriction enzymesBsgI, Eco57I and BpmI.

Other restriction enzymes that cut DNA at a distance from therecognition site, and produce a recessed 3′ end and a 5′ overhanginclude Type III restriction enzymes. For example, the restrictionenzyme EcoP15I recognizes the sequence 5′ CAGCAG 3′ and cleaves 25 basesdownstream on the sense strand and 27 bases on the antisense strand. Itwill be further appreciated by a person of ordinary skill in the artthat new restriction enzymes are continually being discovered and mayreadily be adopted for use in the subject invention.

In another embodiment, the second primer can contain a portion of therecognition sequence for a restriction enzyme, wherein the fullrecognition site for the restriction enzyme is generated uponamplification of the template DNA such that digestion with therestriction enzyme generates a 5′ overhang containing the locus ofinterest. For example, the recognition site for BsmF I is 5′ GGGACN₁₀^(↓)03′. The 3′ region, which anneals to the template DNA, of the secondprimer can end with the nucleotides “GGG,” which do not have to becomplementary with the template DNA. If the 3′ annealing region is about10-20 bases, even if the last three bases do not anneal, the primer willextend and, generate a BsmF I site.

Second primer: 5′ GGAAATTCCATGATGCGTGGG→ (SEQ ID NO:3) Template DNA:3′ CCTTTAAGGTACTACGCAN_(1′)N_(2′)N_(3′)TG 5′5′ GGAAATTCCATGATGCGTN₁N₂N₃AC 3′ (SEQ ID NO:4)

The second primer can be designed to anneal to the template DNA, whereinthe next two bases of the template DNA are thymidine and guanine, suchthat an adenosine and cytosine are incorporated into the primer forminga recognition site for BsmF I, 5′ GGGACN₁₀ ^(↓)03′. The second primercan be designed to anneal in such a manner that digestion with BsmF Igenerates a 5′ overhang containing the locus of interest.

In another embodiment, the second primer can contain an entire or fullrecognition site for a restriction enzyme or a portion of a recognitionsite, which generates a full recognition site upon amplification of thetemplate DNA such that digestion with a restriction enzyme that cuts atthe recognition site generates a 5′ overhang that contains the locus ofinterest. For example, the restriction enzyme BsaJ I binds the followingrecognition site: 5′ C^(↓)CN₁N₂GG 3′. The second primer can be designedsuch that the 3′ region of the primer ends with “CC.” The SNP ofinterest is represented by “N_(1′)”, and the template sequencedownstream of the SNP is “N_(2′)CC.”

Second primer 5′ GGAAATTCCATGATGCGTACC→ (SEQ ID NO:5) Template DNA3′ CCTTTAAGGTACTACGCATGGN_(1′)N_(2′)CC 5′ 5′ GGAAATTCCATGATGCGTACCN₁N₂GG3′  (SEQ ID NO:6)

After digestion with BsaJ I, a 5′ overhang of the following sequencewould be generated:

5′C         3′ 3′GGN_(1′)N_(2′)C 5′

If the nucleotide guanine is not reported at the locus of interest, the3′ recessed end can be filled in with unlabeled cytosine, which iscomplementary to the first nucleotide in the overhang. After removingthe excess cytosine, labeled ddNTPs can be used to fill in the nextnucleotide, N_(1′), which represents the locus of interest.Alternatively if guanine is reported to be a potential nucleotide at thelocus of interest, labeled nucleotides can be used to detect anucleotide 3′ of the locus of interest. Unlabeled dCTP can be used to“fill in” followed by a fill in with a labeled nucleotide other thatcytosine. Cytosine will be incorporated until it reaches a base that isnot complementary. If the locus of interest contained a guanine, itwould be filled in with the dCTP, which would allow incorporation of thelabeled nucleotide. However, if the locus of interest did not contain aguanine, the labeled nucleotide would not be incorporated. Otherrestriction enzymes can be used including but not limited to BssK I (5′^(↓)CCNGG 3′), Dde I (5′ C^(↓)TNAG 3′), EcoN I (5′ CCTNN^(↓)NNNAGG 3′)(SEQ ID NO:7), Fnu4H I (5′ GC^(↓)NGC 3′), Hinf I (5′ G^(↓)ANTC 3′), Pf1FI (5′ GACN^(↓)NNGTC 3′), Sau96 I (5′ G^(↓)GNCC 3′), ScrF I (5′ CC^(↓)NGG3′), and Tth111 I (5′ GACN^(↓)NNGTC 3′).

It is not necessary that the 3′ region, which anneals to the templateDNA, of the second primer be 100% complementary to the template DNA. Forexample, the last 1, 2, or 3 nucleotides of the 3′ end of the secondprimer can be mismatches with the template DNA. The region of the primerthat anneals to the template DNA will target the primer, and allow theprimer to extend. Even if, for example, the last two nucleotides are notcomplementary to the template DNA, the primer will extend and generate arestriction enzyme recognition site.

Second primer: 5′ GGAAATTCCATGATGCGTACC→ (SEQ ID NO:5) Template DNA:3′ CCTTTAAGGTACTACGCATN_(a′)N_(b′)N_(1′)N_(2′)CC 5′5′ GGAAATTCCATGATGCGTAN_(a)N_(b)N₁N₂GG 3′ (SEQ ID NO:8)

After digestion with BsaJ I, a 5′ overhang of the following sequencewould be generated:

5′ C         3′ 3′ GGN_(1′)N_(2′)C 5′

If the nucleotide cytosine is not reported at the locus of interest, the5′ overhang can be filled in with unlabeled cytosine. The excesscytosine can be rinsed away, and filled in with labeled ddNTPs. Thefirst nucleotide incorporated (N₁) corresponds to the locus of interest.

Alternatively, it is possible to create the full restriction enzymerecognition sequence using the first and second primers. The recognitionsite for any restriction enzyme can be generated, as long as therecognition site contains at least one variable nucleotide. Restrictionenzymes that recognize sites that contain at least one variablenucleotide include but are not limited to BssK I (5′^(↓)CCNGG 3′), Dde I(5′C^(↓)TNAG 3′), Econ I (5′CCTNN^(↓)NNNAGG 3′) (SEQ ID NO:7), Fnu4H I(5′GC^(↓)NGC 3′), Hinf I (5′G^(↓)ANTC 3′) Pf1F I (5′ GACN^(↓)NNGTC 3′),Sau96 I (5′G^(↓)GNCC 3′), ScrF I (5′ CC^(↓)NGG 3′), and Tth111 I (5′GACN^(↓)NNGTC 3′). In this embodiment, the first or second primer mayanneal closer to the locus of interest or the first or second primer mayanneal at an equal distance from the locus of interest. The first andsecond primers can be designed to contain mismatches to the template DNAat the 3′ region; these mismatches create the restriction enzymerecognition site. The number of mismatches that can be tolerated at the3′ end depends on the length of the primer, and includes but is notlimited to 1, 2, or more than 2 mismatches. For example, if the locus ofinterest is represented by N_(1′), a first primer can be designed to becomplementary to the template DNA, depicted below as region “a.” The 3′region of the first primer ends with “CC,” which is not complementary tothe template DNA. The second primer is designed to be complementary tothe template DNA, which is depicted below as region “b′”. The 3′ regionof the second primer ends with “CC,” which is not complementary to thetemplate DNA.

First primer 5′  a CC→ Template DNA 3′   a′    AAN_(1′)N_(2′)TT  b′   5′5′   a  TTN₁N₂AA  b  3′             ←CC  b′   5′  Second                        Primer

After one round of amplification the following products would begenerated:

5′  a  CCN₁N₂AA  b  3′ and 5′  b′  CCN_(2′)N_(1′)AA  a′  3′.

In cycle two, the primers can anneal to the templates that weregenerated from the first cycle of PCR:

5′  a  CCN₁N₂AA  b  3′             ←CC  b′  5′             ←CC  a  5′5′  b′  CCN_(2′)N_(1′)AA  a′  3′

After cycle two of PCR, the following products would be generated:

5′  a  CCN₁N₂GG  b  3′ 3′  a′ GGN_(1′)N_(2′)CC  b′ 5′The restriction enzyme recognition site for BsaJ I is generated, andafter digestion with BsaJ I, a 5′ overhang containing the locus ofinterest is generated. The locus of interest can be detected asdescribed in detail below. Alternatively, the 3′ region of the first andsecond primers can contain 1, 2, 3, or more than 3 mismatches followedby a nucleotide that is complementary to the template DNA. For example,the first and second primers can be used to create a recognition sitefor the restriction enzyme EcoN I, which binds the following DNAsequence: 5′ CCTNN^(↓)NNNAGG 3′. The last nucleotides of each primerwould be “CCTN₁ or CCTN₁N₂.” The nucleotides “CCT” may or may not becomplementary to the template DNA; however, N₁ and N₂ are nucleotidescomplementary to the template DNA. This allows the primers to anneal tothe template DNA after the potential mismatches, which are used tocreate the restriction enzyme recognition site.

In another embodiment, a primer pair has sequence at the 5′ region ofeach of the primers that provides two or more restriction sites that arerecognized by two or more restriction enzymes.

In a most preferred embodiment, a primer pair has different restrictionenzyme recognition sites at the 5′ regions, especially 5′ ends, suchthat a different restriction enzyme is required to cleave away anyundesired sequences. For example, the first primer for locus of interest“A” can contain sequence recognized by a restriction enzyme, “X,” whichcan be any type of restriction enzyme, and the second primer for locusof interest “A,” which anneals closer to the locus of interest, cancontain sequence for a restriction enzyme, “Y,” which is a Type IISrestriction enzyme that cuts “n” nucleotides away and leaves a 5′overhang and a recessed 3′ end. The 5′ overhang contains the locus ofinterest. After binding the amplified DNA to streptavidin coated wells,one can digest with enzyme “Y,” rinse, then fill in with labelednucleotides and rinse, and then digest with restriction enzyme “X,”which will release the DNA fragment containing the locus of interestfrom the solid matrix. The locus of interest can be analyzed bydetecting the labeled nucleotide that was “filled in” at the locus ofinterest, e.g. SNP site.

In another embodiment, the second primers for the different loci ofinterest that are being amplified according to the invention containrecognition sequence in the 5′ regions for the same restriction enzymeand likewise all the first primers also contain the same restrictionenzyme recognition site, which is a different enzyme from the enzymethat recognizes the second primers. The primer (either the forward orreverse primer) that anneals closer to the locus of interest contains arecognition site for, e.g., a Type IIs restriction enzyme.

In another embodiment, the second primers for the multiple loci ofinterest that are being amplified according to the invention containrestriction enzyme recognition sequences in the 5′ regions for differentrestriction enzymes.

In another embodiment, the first primers for the multiple loci ofinterest that are being amplified according to the invention containrestriction enzyme recognition sequences in the 5′ regions for differentrestriction enzymes.

Multiple restriction enzyme sequences provide an opportunity toinfluence the order in which pooled loci of interest are released fromthe solid support. For example, if 50 loci of interest are amplified,the first primers can have a tag at the extreme 5′ end to aid inpurification and a restriction enzyme recognition site, and the secondprimers can contain a recognition site for a type IIS restrictionenzyme. For example, several of the first primers can have a restrictionenzyme recognition site for EcoR I, other first primers can have arecognition site for Pst I, and still other first primers can have arecognition site for BamH I. After amplification, the loci of interestcan be bound to a solid support with the aid of the tag on the firstprimers. By performing the restriction digests one restriction enzyme ata time, one can serially release the amplified loci of interest. If thefirst digest is performed with EcoRI, the loci of interest amplifiedwith the first primers containing the recognition site for EcoR I willbe released, and collected while the other loci of interest remain boundto the solid support. The amplified loci of interest can be selectivelyreleased from the solid support by digesting with one restriction enzymeat a time. The use of different restriction enzyme recognition sites inthe first primers allows a larger number of loci of interest to beamplified in a single reaction tube.

In a preferred embodiment, any region 5′ of the restriction enzymedigestion site of each primer can be modified with a functional groupthat provides for fragment manipulation, processing, identification,and/or purification. Examples of such functional groups, or tags,include but are not limited to biotin, derivatives of biotin,carbohydrates, haptens, dyes, radioactive molecules, antibodies, andfragments of antibodies, peptides, and immunogenic molecules.

In another embodiment, the template DNA can be replicated once, withoutbeing amplified beyond a single round of replication. This is usefulwhen there is a large amount of the DNA available for analysis such thata large number of copies of the loci of interest are already present inthe sample, and further copies are not needed. In this embodiment, theprimers are preferably designed to contain a “hairpin” structure in the5′ region, such that the sequence doubles back and anneals to a sequenceinternal to itself in a complementary manner. When the template DNA isreplicated only once, the DNA sequence comprising the recognition sitewould be single-stranded if not for the “hairpin” structure. However, inthe presence of the hairpin structure, that region is effectively doublestranded, thus providing a double stranded substrate for activity byrestriction enzymes.

To the extent that the reaction conditions are compatible, all theprimer pairs to analyze a locus or loci of interest of DNA can be mixedtogether for use in the method of the invention. In a preferredembodiment, all primer pairs are mixed with the template DNA in a singlereaction vessel. Such a reaction vessel can be, for example, a reactiontube, or a well of a microtiter plate.

Alternatively, to avoid competition for nucleotides and to minimizeprimer dimers and difficulties with annealing temperatures for primers,each locus of interest or small groups of loci of interest can beamplified in separate reaction tubes or wells, and the products laterpooled if desired. For example, the separate reactions can be pooledinto a single reaction vessel before digestion with the restrictionenzyme that generates a 5′ overhang, which contains the locus ofinterest or SNP site, and a 3′ recessed end. Preferably, the primers ofeach primer pair are provided in equimolar amounts. Also, especiallypreferably, each of the different primer pairs is provided in equimolaramounts relative to the other pairs that are being used.

In another embodiment, combinations of primer pairs that allow efficientamplification of their respective loci of interest can be used (see e.g.FIG. 2). Such combinations can be determined prior to use in the methodof the invention. Multi-well plates and PCR machines can be used toselect primer pairs that work efficiently with one another. For example,gradient PCR machines, such as the Eppendorf Mastercycler® gradient PCRmachine, can be used to select the optimal annealing temperature foreach primer pair. Primer pairs that have similar properties can be usedtogether in a single reaction tube.

In another embodiment, a multi-sample container including but notlimited to a 96-well or more plate can be used to amplify a single locusof interest with the same primer pairs from multiple template DNAsamples with optimal PCR conditions for that locus of interest.Alternatively, a separate multi-sample container can be used foramplification of each locus of interest and the products for eachtemplate DNA sample later pooled. For example, gene A from 96 differentDNA samples can be amplified in microtiter plate 1, gene B from 96different DNA samples can be amplified in microtiter plate 2, etc., andthen the amplification products can be pooled.

The result of amplifying multiple loci of interest is a preparation thatcontains representative PCR products having the sequence of each locusof interest. For example, if DNA from only one individual is used as thetemplate DNA and if hundreds of disease-related loci of interest wereamplified from the template DNA, the amplified DNA would be a mixture ofsmall, PCR products from each of the loci of interest. Such apreparation could be further analyzed at that time to determine thesequence at each locus of interest or at only some of loci of interest.Additionally, the preparation could be stored in a manner that preservesthe DNA and can be analyzed at a later time. Information contained inthe amplified DNA can be revealed by any suitable method including butnot limited to fluorescence detection, sequencing, gel electrophoresis,and mass spectrometry (see “Detection of Incorporated Nucleotide”section below).

Amplification of Loci of Interest

The template DNA can be amplified using any suitable method known in theart including but not limited to PCR (polymerase chain reaction), 3SR(self-sustained sequence reaction), LCR (ligase chain reaction),RACE-PCR (rapid amplification of cDNA ends), PLCR (a combination ofpolymerase chain reaction and ligase chain reaction), Q-beta phageamplification (Shah et al., J. Medical Micro. 33: 1435-41 (1995)), SDA(strand displacement amplification), SOE-PCR (splice overlap extensionPCR), and the like. These methods can be used to design variations ofthe releasable primer mediated cyclic amplification reaction explicitlydescribed in this application. In the most preferred embodiment, thetemplate DNA is amplified using PCR (PCR: A Practical Approach, M. J.McPherson, et al., IRL Press (1991); PCR Protocols: A Guide to Methodsand Applications, Innis, et al., Academic Press (1990); and PCRTechnology: Principals and Applications of DNA Amplification, H. A.Erlich, Stockton Press (1989)). PCR is also described in numerous U.S.patents, including U.S. Pat. Nos. 4,683,195; 4,683,202; 4,800,159;4,965,188; 4,889,818; 5,075,216; 5,079,352; 5,104,792, 5,023,171;5,091,310; and 5,066,584.

The components of a typical PCR reaction include but are not limited toa template DNA, primers, a reaction buffer (dependent on choice ofpolymerase), dNTPs (dATP, dTTP, dGTP, and dCTP) and a DNA polymerase.Suitable PCR primers can be designed and prepared as discussed above(see “Primer Design” section above). Briefly, the reaction is heated to95° C. for 2 min. to separate the strands of the template DNA, thereaction is cooled to an appropriate temperature (determined bycalculating the annealing temperature of designed primers) to allowprimers to anneal to the template DNA, and heated to 72° C. for twominutes to allow extension.

In a preferred embodiment, the annealing temperature is increased ineach of the first three cycles of amplification to reduce non-specificamplification. See also Example 1, below. The TM1 of the first cycle ofPCR is about the melting temperature of the 3′ region of the secondprimer that anneals to the template DNA. The annealing temperature canbe raised in cycles 2-10, preferably in cycle 2, to TM2, which is aboutthe melting temperature of the 3′ region, which anneals to the templateDNA, of the first primer. If the annealing temperature is raised incycle 2, the annealing temperature remains about the same until the nextincrease in annealing temperature. Finally, in any cycle subsequent tothe cycle in which the annealing temperature was increased to TM2,preferably cycle 3, the annealing temperature is raised to TM3, which isabout the melting temperature of the entire second primer. After thethird cycle, the annealing temperature for the remaining cycles may beat about TM3 or may be further increased. In this example, the annealingtemperature is increased in cycles 2 and 3. However, the annealingtemperature can be increased from a low annealing temperature in cycle 1to a high annealing temperature in cycle 2 without any further increasesin temperature or the annealing temperature can progressively changefrom a low annealing temperature to a high annealing temperature in anynumber of incremental steps. For example, the annealing temperature canbe changed in cycles 2, 3, 4, 5, 6, etc.

After annealing, the temperature in each cycle is increased to an“extension” temperature to allow the primers to “extend” and thenfollowing extension the temperature in each cycle is increased to thedenaturization temperature. For PCR products less than 500 base pairs insize, one can eliminate the extension step in each cycle and just havedenaturization and annealing steps. A typical PCR reaction consists of25-45 cycles of denaturation, annealing and extension as describedabove. However, as previously noted, even only one cycle ofamplification (one copy) can be sufficient for practicing the invention.

Any DNA polymerase that catalyzes primer extension can be used includingbut not limited to E. coli DNA polymerase, Klenow fragment of E. coliDNA polymerase I, T7 DNA polymerase, T4 DNA polymerase, Taq polymerase,Pfu DNA polymerase, Vent DNA polymerase, or sequenase. Preferably, athermostable DNA polymerase is used. A “hot start” PCR can also beperformed wherein the reaction is heated to 95° C. for two minutes priorto addition of the polymerase or the polymerase can be kept inactiveuntil the first heating step in cycle 1. “Hot start” PCR can be used tominimize nonspecific amplification. Any number of PCR cycles can be usedto amplify the DNA, including but not limited to 2, 5, 10, 15, 20, 25,30, 35, 40, or 45 cycles. In a most preferred embodiment, the number ofPCR cycles performed is such that equimolar amounts of each loci ofinterest are produced.

Purification of Amplified DNA

Purification of the amplified DNA is not necessary for practicing theinvention. However, in one embodiment, if purification is preferred, the5′ end of the primer (first or second primer) can be modified with a tagthat facilitates purification of the PCR products. In a preferredembodiment, the first primer is modified with a tag that facilitatespurification of the PCR products. The modification is preferably thesame for all primers, although different modifications can be used if itis desired to separate the PCR products into different groups.

The tag can be a radioisotope, fluorescent reporter molecule,chemiluminescent reporter molecule, antibody, antibody fragment, hapten,biotin, derivative of biotin, photobiotin, iminobiotin, digoxigenin,avidin, enzyme, acridinium, sugar, enzyme, apoenzyme, homopolymericoligonucleotide, hormone, ferromagnetic moiety, paramagnetic moiety,diamagnetic moiety, phosphorescent moiety, luminescent moiety,electrochemiluminescent moiety, chromatic moiety, moiety having adetectable electron spin resonance, electrical capacitance, dielectricconstant or electrical conductivity, or combinations thereof.

In a preferred embodiment, the 5′ ends of the primers can bebiotinylated (Kandpal et al., Nucleic Acids Res. 18:1789-1795 (1990);Kaneoka et al., Biotechniques 10:30-34 (1991); Green et al., NucleicAcids Res. 18:6163-6164 (1990)). The biotin provides an affinity tagthat can be used to purify the copied DNA from the genomic DNA or anyother DNA molecules that are not of interest. Biotinylated molecules canbe purified using a streptavidin coated matrix as shown in FIG. 1F,including but not limited to Streptawell, transparent, High-Bind platesfrom Roche Molecular Biochemicals (catalog number 1 645 692, as listedin Roche Molecular Biochemicals, 2001 Biochemicals Catalog).

The PCR product of each locus of interest is placed into separate wellsof a Streptavidin coated plate. Alternatively, the PCR products of theloci of interest can be pooled and placed into a streptavidin coatedmatrix, including but not limited to the Streptawell, transparent,High-Bind plates from Roche Molecular Biochemicals (catalog number 1 645692, as listed in Roche Molecular Biochemicals, 2001 BiochemicalsCatalog).

The amplified DNA can also be separated from the template DNA usingnon-affinity methods known in the art, for example, by polyacrylamidegel electrophoresis using standard protocols.

Digestion of Amplified DNA

The amplified DNA can be digested with a restriction enzyme thatrecognizes a sequence that had been provided on the first or secondprimer using standard protocols known within the art (FIGS. 6A-6D). Theenzyme used depends on the restriction recognition site generated withthe first or second primer. See “Primer Design” section, above, fordetails on restriction recognition sites generated on primers.

Type IIS restriction enzymes are extremely useful in that they cutapproximately 10-20 base pairs outside of the recognition site.Preferably, the Type IIS restriction enzymes used are those thatgenerate a 5′ overhang and a recessed 3′ end, including but not limitedto BceA I and BsmF I (see e.g. Table I). In a most preferred embodiment,the second primer (either forward or reverse), which anneals close tothe locus of interest, contains a restriction enzyme recognitionsequence for BsmF I or BceA I. The Type IIS restriction enzyme BsmF Irecognizes the nucleic acid sequence GGGAC, and cuts 14 nucleotides fromthe recognition site on the antisense strand and 10 nucleotides from therecognition site on the sense strand. Digestion with BsmF I generates a5′ overhang of four (4) bases.

For example, if the second primer is designed so that afteramplification the restriction enzyme recognition site is 13 bases fromthe locus of interest, then after digestion, the locus of interest isthe first base in the 5′ overhang (reading 3′ to 5′), and the recessed3′ end is one base upstream of the locus of interest. The 3′ recessedend can be filled in with a nucleotide that is complementary to thelocus of interest. One base of the overhang can be filled in usingdideoxynucleotides. However, 1, 2, 3, or all 4 bases of the overhang canbe filled in using deoxynucleotides or a mixture of dideoxynucleotidesand deoxynucleotides.

The restriction enzyme BsmF I cuts DNA ten (10) nucleotides from therecognition site on the sense strand and fourteen (14) nucleotides fromthe recognition site on the antisense strand. However, in a sequencedependent manner, the restriction enzyme BsmF I also cuts eleven (11)nucleotides from the recognition site on the sense strand and fifteen(15) nucleotides from the recognition site on the antisense strand.Thus, two populations of DNA molecules exist after digestion: DNAmolecules cut at 10/14 and DNA molecules cut at 11/15. If therecognition site for BsmF I is 13 bases from the locus of interest inthe amplified product, then DNA molecules cut at the 11/15 position willgenerate a 5′ overhang that contains the locus of interest in the secondposition of the overhang (reading 3′ to 5′). The 3′ recessed end of theDNA molecules can be filled in with labeled nucleotides. For example, iflabeled dideoxynucleotides are used, the 3′ recessed end of themolecules cut at 11/15 would be filled in with one base, whichcorresponds to the base upstream of the locus of interest, and the 3′recessed end of molecules cut at 10/14 would be filled in with one base,which corresponds to the locus of interest. The DNA molecules that havebeen cut at the 10/14 position and the DNA molecules that have been cutat the 11/15 position can be separated by size, and the incorporatednucleotides detected. This allows detection of both the nucleotidebefore the locus of interest, detection of the locus of interest, andpotentially the three bases pairs after the locus of interest.

Alternatively, if the base upstream of the locus of interest and thelocus of interest are different nucleotides, then the 3′ recessed end ofthe molecules cut at 11/15 can be filled in with deoxynucleotide that iscomplementary to the upstream base. The remaining deoxynucleotide iswashed away, and the locus of interest site can be filled in with eitherlabeled deoxynucleotides, unlabeled deoxynucleotides, labeleddideoxynucleotides, or unlabeled dideoxynucleotides. After the fill inreaction, the nucleotide can be detected by any suitable method. Thus,after the first fill in reaction with dNTP, the 3′recessed end of themolecules cut at 10/14 and 11/15 is upstream of the locus of interest.The 3′ recessed end can now be filled in one base, which corresponds tothe locus of interest, two bases, three bases or four bases.

Alternatively, if the base upstream of the locus of interest and thebase downstream of the locus of interest are reported to be the same,the 3′ recessed end of the molecules cut at 11/15 can be “filled in”with unlabeled deoxynucleotide, followed by a “fill in” with labeleddideoxynucleotide. For example, if the nucleotide upstream of the locusof interest is a cytosine, and a cytosine is a potential nucleotide atthe locus of interest, and an adenosine is the first nucleotide 3′ ofthe locus of interest, a “fill in” reaction can be performed withunlabeled deoxyguanine triphosphate (dGTP), followed by a fill in withlabeled dideoxythymidine triphosphate. If the locus of interest containsa cytosine, the ddTTP will be incorporated and detected. However, if thelocus of interest does not contain a cytosine, the dGTP will not beincorporated, which prevents incorporation of the ddTTP.

The restriction enzyme BceA I recognizes the nucleic acid sequence ACGGCand cuts 12 (twelve) nucleotides from the recognition site on the sensestrand and 14 (fourteen) nucleotides from the recognition site on theantisense strand. If the distance from the recognition site for BceA Ion the second primer is designed to be thirteen (13) bases from thelocus of interest (see FIGS. 4A-4D), digestion with BceA I will generatea 5′ overhang of two bases, which contains the locus of interest, and arecessed 3′ end that is upstream of the locus of interest. The locus ofinterest is the first nucleotide in the 5′ overhang (reading 3′ to 5′).

Alternative cutting is also seen with the restriction enzyme BceA I,although at a much lower frequency than is seen with BsmF I. Therestriction enzyme BceA I can cut thirteen (13) nucleotides from therecognition site on the sense strand and fifteen (15) nucleotides fromthe recognition site on the antisense strand. Thus, two populations ofDNA molecules exist: DNA molecules cut at 12/14 and DNA molecules cut at13/15. If the restriction enzyme recognition site is 13 bases from thelocus of interest in the amplified product, DNA molecules cut at the13/15 position yield a 5′ overhang, which contains the locus of interestin the second position of the overhang (reading 3′ to 5′). Labeleddideoxynucleotides can be used to fill in the 3′ recessed end of the DNAmolecules. The DNA molecules cut at 13/15 will have the base upstream ofthe locus of interest filled in, and the DNA molecules cut at 12/14 willhave the locus of interest site filled in. The DNA molecules cut at13/15 and those cut at 12/14 can be separated by size, and theincorporated nucleotide detected. Thus, the alternative cutting can beused to obtain additional sequence information.

Alternatively, if the two bases in the 5′ overhang are different, the 3′recessed end of the DNA molecules, which were cut at 13/15, can befilled in with the deoxynucleotide complementary to the first base inthe overhang, and excess deoxynucleotide washed away. After filling in,the 3′ recessed end of the DNA molecules that were cut at 12/14 and theDNA molecules that were cut at 13/15 are upstream of the locus ofinterest. The 3′ recessed ends can be filled with either labeleddideoxynucleotides, unlabeled dideoxynucleotides, labeleddeoxynucleotides, or unlabeled deoxynucleotides.

If the primers provide different restriction sites for certain of theloci of interest that were copied, all the necessary restriction enzymescan be added together to digest the copied DNA simultaneously.Alternatively, the different restriction digests can be made insequence, for example, using one restriction enzyme at a time, so thatonly the product that is specific for that restriction enzyme isdigested.

Incorporation of Labeled Nucleotides

Digestion with the restriction enzyme that recognizes the sequence onthe second primer generates a recessed 3′ end and a 5′ overhang, whichcontains the locus of interest (FIG. 1G). The recessed 3′ end can befilled in using the 5′ overhang as a template in the presence ofunlabeled or labeled nucleotides or a combination of both unlabeled andlabeled nucleotides. The nucleotides can be labeled with any type ofchemical group or moiety that allows for detection including but notlimited to radioactive molecules, fluorescent molecules, antibodies,antibody fragments, haptens, carbohydrates, biotin, derivatives ofbiotin, phosphorescent moieties, luminescent moieties,electrochemiluminescent moieties, chromatic moieties, and moietieshaving a detectable electron spin resonance, electrical capacitance,dielectric constant or electrical conductivity. The nucleotides can belabeled with one or more than one type of chemical group or moiety. Eachnucleotide can be labeled with the same chemical group or moiety.Alternatively, each different nucleotide can be labeled with a differentchemical group or moiety. The labeled nucleotides can be dNTPs, ddNTPs,or a mixture of both dNTPs and ddNTPs. The unlabeled nucleotides can bedNTPs, ddNTPs or a mixture of both dNTPs and ddNTPs.

Any combination of nucleotides can be used to incorporate nucleotidesincluding but not limited to unlabeled deoxynucleotides, labeleddeoxynucleotides, unlabeled dideoxynucleotides, labeleddideoxynucleotides, a mixture of labeled and unlabeled deoxynucleotides,a mixture of labeled and unlabeled dideoxynucleotides, a mixture oflabeled deoxynucleotides and labeled dideoxynucleotides, a mixture oflabeled deoxynucleotides and unlabeled dideoxynucleotides, a mixture ofunlabeled deoxynucleotides and unlabeled dideoxynucleotides, a mixtureof unlabeled deoxynucleotides and labeled dideoxynucleotides,dideoxynucleotide analogues, deoxynucleotide analogues, a mixture ofdideoxynucleotide analogues and deoxynucleotide analogues,phosphorylated nucleoside analogues, 2-deoxynucleoside-5′ triphosphatesand modified 2′-deoxynucleoside triphosphates.

For example, as shown in FIG. 1H, in the presence of a polymerase, the3′ recessed end can be filled in with fluorescent ddNTP using the 5′overhang as a template. The incorporated ddNTP can be detected using anysuitable method including but not limited to fluorescence detection.

All four nucleotides can be labeled with different fluorescent groups,which will allow one reaction to be performed in the presence of allfour labeled nucleotides. Alternatively, five separate “fill in”reactions can be performed for each locus of interest; each of the fourreactions will contain a different labeled nucleotide (e.g. ddATP*,ddTTP*, ddUTP*, ddGTP*, or ddCTP*, where * indicates a labelednucleotide). Each nucleotide can be labeled with different chemicalgroups or the same chemical groups. The labeled nucleotides can bedideoxynucleotides or deoxynucleotides.

In another embodiment, nucleotides can be labeled with fluorescent dyesincluding but not limited to fluorescein, pyrene, 7-methoxycoumarin,Cascade Blue.TM., Alexa Flur 350, Alexa Flur 430, Alexa Flur 488, AlexaFlur 532, Alexa Flur 546, Alexa Flur 568, Alexa Flur 594, Alexa Flur633, Alexa Flur 647, Alexa Flur 660, Alexa Flur 680, AMCA-X,dialkylaminocoumarin, Pacific Blue, Marina Blue, BODIPY 493/503, BODIPYFl-X, DTAF, Oregon Green 500, Dansyl-X, 6-FAM, Oregon Green 488, OregonGreen 514, Rhodamine Green-X, Rhodol Green, Calcein, Eosin, ethidiumbromide, NBD, TET, 2′, 4′, 5′, 7′ tetrabromosulfonefluorescien,BODIPY-R6G, BODIPY-Fl BR2, BODIPY 530/550, HEX, BODIPY 558/568,BODIPY-TMR-X., PyMPO, BODIPY 564/570, TAMRA, BODIPY 576/589, Cy3,Rhodamine Red-x, BODIPY 581/591, carboxyXrhodamine, Texas Red-X,BODIPY-TR-X., Cy5, SpectrumAqua, SpectrumGreen #1, SpectrumGreen #2,SpectrumOrange, SpectrumRed, or naphthofluorescein.

In another embodiment, the “fill in” reaction can be performed withfluorescently labeled dNTPs, wherein the nucleotides are labeled withdifferent fluorescent groups. The incorporated nucleotides can bedetected by any suitable method including but not limited toFluorescence Resonance Energy Transfer (FRET).

In another embodiment, a mixture of both labeled ddNTPs and unlabeleddNTPs can be used for filling in the recessed 3′ end of the SNP or locusof interest. Preferably, the 5′ overhang consists of more than one base,including but not limited to 2, 3, 4, 5, 6 or more than 6 bases. Forexample, if the 5′ overhang consists of the sequence “XGAA,” wherein Xis the locus of interest, e.g. SNP, then filling in with a mixture oflabeled ddNTPs and unlabeled dNTPs will produce several different DNAfragments. If a labeled ddNTP is incorporated at position “X,” thereaction will terminate and a single labeled base will be incorporated.If however, an unlabeled dNTP is incorporated, the polymerase continuesto incorporate other bases until a labeled ddNTP is incorporated. If thefirst two nucleotides incorporated are dNTPs, and the third is a ddNTP,the 3′ recessed end will be extend by three bases. This DNA fragment canbe separated from the other DNA fragments that were extended by 1, 2, or4 bases by size. A mixture of labeled ddNTPs and unlabeled dNTPs willallow all bases of the overhang to be filled in, and provides additionalsequence information about the locus of interest, e.g. SNP (see FIGS. 7Eand 9D).

After incorporation of the labeled nucleotide, the amplified DNA can bedigested with a restriction enzyme that recognizes the sequence providedby the first primer. For example, in FIG. 1I, the amplified DNA isdigested with a restriction enzyme that binds to region “a,” whichreleases the DNA fragment containing the incorporated nucleotide fromthe streptavidin matrix.

Alternatively, one primer of each primer pair for each locus of interestcan be attached to a solid support matrix including but not limited to awell of a microtiter plate. For example, streptavidin-coated microtiterplates can be used for the amplification reaction with a primer pair,wherein one primer is biotinylated. First, biotinylated primers arebound to the streptavidin-coated microtiter plates. Then, the plates areused as the reaction vessel for PCR amplification of the loci ofinterest. After the amplification reaction is complete, the excessprimers, salts, and template DNA can be removed by washing. Theamplified DNA remains attached to the microtiter plate. The amplifiedDNA can be digested with a restriction enzyme that recognizes a sequenceon the second primer and generates a 5′ overhang, which contains thelocus of interest. The digested fragments can be removed by washing.After digestion, the SNP site or locus of interest is exposed in the 5′overhang. The recessed 3′ end is filled in with a labeled nucleotide,including but not limited to, fluorescent ddNTP in the presence of apolymerase. The labeled DNA can be released into the supernatant in themicrotiter plate by digesting with a restriction enzyme that recognizesa sequence in the 5′ region of the first primer.

Analysis of the Locus of Interest

The labeled loci of interest can be analyzed by a variety of methodsincluding but not limited to fluorescence detection, DNA sequencing gel,capillary electrophoresis on an automated DNA sequencing machine,microchannel electrophoresis, and other methods of sequencing, massspectrometry, time of flight mass spectrometry, quadrupole massspectrometry, magnetic sector mass spectrometry, electric sector massspectrometry infrared spectrometry, ultraviolet spectrometry,palentiostatic amperometry or by DNA hybridization techniques includingSouthern Blots, Slot Blots, Dot Blots, and DNA microarrays, wherein DNAfragments would be useful as both “probes” and “targets,” ELISA,fluorimetry, and Fluorescence Resonance Energy Transfer (FRET).

The loci of interest can be analyzed using gel electrophoresis followedby fluorescence detection of the incorporated nucleotide. Another methodto analyze or read the loci of interest is to use a fluorescent platereader or fluorimeter directly on the 96-well streptavidin coatedplates. The plate can be placed onto a fluorescent plate reader orscanner such as the Pharmacia 9200 Typhoon to read each locus ofinterest.

Alternatively, the PCR products of the loci of interest can be pooledand after “filling in,” (FIG. 10) the products can be separated by size,using any method appropriate for the same, and then analyzed using avariety of techniques including but not limited to fluorescencedetection, DNA sequencing gel, capillary electrophoresis on an automatedDNA sequencing machine, microchannel electrophoresis, other methods ofsequencing, DNA hybridization techniques including Southern Blots, SlotBlots, Dot Blots, and DNA microarrays, mass spectrometry, time of flightmass spectrometry, quadrupole mass spectrometry, magnetic sector massspectrometry, electric sector mass spectrometry infrared spectrometry,ultraviolet spectrometry, palentiostatic amperometry. For example,polyacrylamide gel electrophoresis can be used to separate DNA by sizeand the gel can be scanned to determine the color of fluorescence ineach band (using e.g. ABI 377 DNA sequencing machine or a PharmaciaTyphoon 9200).

In another embodiment, the sequence of the locus of interest can bedetermined by detecting the incorporation of a nucleotide that is 3′ tothe locus of interest provided it is a different nucleotide from thepossible nucleotides at the locus of interest. This embodiment isespecially useful for the sequencing and detection of SNPs. Theefficiency and rate at which DNA polymerases incorporate nucleotidesvaries for each nucleotide. However, one labeled nucleotide can be usedto detect the nucleotide at the locus of interest.

According to the data from the Human Genome Project, 99% of all SNPs arebinary. The sequence of the human genome can be used to determine thenucleotide that is 3′ to the SNP of interest. When the nucleotide thatis 3′ to the SNP site differs from the possible nucleotides at the SNPsite, a nucleotide that is one or more than one base 3′ to the SNP canbe used to determine the sequence of the SNP.

For example, suppose the sequence of SNP X on chromosome 13 is to bedetermined. The sequence of the human genome indicates that SNP X caneither be adenosine or guanine and that the 3′ nucleotide is thymidine.A primer that contains a restriction enzyme recognition site for BsmF I,which is designed to be 13 bases from the locus of interest afteramplification, is used to amplify SNP X. Digestion with the restrictionenzyme BsmF I generates a 5′ overhang that contains the locus ofinterest, which can either be adenosine or guanine. If the nucleotidedownstream (3′) of the locus of interest is different from the possiblenucleotides at the SNP site, the digestion products can be split intotwo “fill in” reactions: one contains dTTP, and the other reactioncontains dCTP. If the locus of interest is homozygous for guanine, onlythe DNA molecules that were mixed with dCTP will be filled in. If thelocus of interest is homozygous for adenosine, only the DNA moleculesthat were mixed with dTTP will be filled in. If the locus of interest isheterozygous, the DNA molecules that were mixed with dCTP will be filledin as well as the DNA molecules that were mixed with dTTP. After washingto remove the excess dNTP, the samples are filled in with labeled ddATP,which is complimentary to the nucleotide (thymidine) that is 3′ to thelocus of interest. The DNA molecules that were filled in by the previousreaction will be filled in with labeled ddATP. If the individual ishomozygous for adenosine, the DNA molecules that were mixed with dTTPsubsequently will be filled in with the labeled ddATP. However, the DNAmolecules that were mixed with dCTP, would not have incorporated thatnucleotide, and therefore, could not incorporate the ddATP. Detection oflabeled ddATP only in the molecules that were mixed with dTTP indicatesthat the nucleotide at SNP X on chromosome 13 is adenosine. Thus, onelabeled nucleotide can be used to detect heterozygous populations ofloci of interest.

In another embodiment, large scale screening for the presence or absenceof single nucleotide mutations can be performed. One to tens to hundredsto thousands of loci of interest on a single chromosome or on multiplechromosomes can be amplified with primers as described above in the“Primer Design” section. The primers can be designed so that eachamplified loci of interest is of a different size (FIG. 2). Theamplified loci of interest that are predicted, based on the publishedwild type sequences, to have the same nucleotide at the locus ofinterest can be pooled together, bound to a solid support, includingwells of a microtiter plate coated with streptavidin, and digested withthe restriction enzyme that will bind the recognition site on the secondprimer. After digestion, the 3′ recessed end can be filled in with amixture of labeled ddATP, ddTTP, ddGTP, ddCTP, where each nucleotide islabeled with a different group. After washing to remove the excessnucleotide, the fluorescence spectra can be detected using a platereader or fluorimeter directly on the streptavidin coated plates. If all50 loci of interest contain the wild type nucleotide, only onefluorescence spectra will be seen. However, if one or more than one ofthe 50 loci of interest contain a mutation, a different nucleotide willbe incorporated and other fluorescence pattern(s) will be seen. Thenucleotides can be released from the solid matrix, and analyzed on asequencing gel to determine the loci of interest that contained themutations. As each of the 50 loci of interest are of different size,they will separate on a sequencing gel.

The multiple loci of interest can be of a DNA sample from one individualrepresenting multiple loci of interest on a single chromosome, multiplechromosomes, multiple genes, a single gene, or any combination thereof.The multiple loci of interest also can represent the same locus ofinterest but from multiple individuals. For example, 50 DNA samples from50 different individuals can be pooled and analyzed to determine aparticular nucleotide of interest at gene “X.”

When human data is being analyzed, the known sequence can be a specificsequence that has been determined from one individual (including e.g.the individual whose DNA is currently being analyzed), or it can be aconsensus sequence such as that published as part of the human genome.

Kits

The methods of the invention are most conveniently practiced byproviding the reagents used in the methods in the form of kits. A kitpreferably contains one or more of the following components: writteninstructions for the use of the kit, appropriate buffers, salts, DNAextraction detergents, primers, nucleotides, labeled nucleotides, 5′ endmodification materials, and if desired, water of the appropriate purity,confined in separate containers or packages, such components allowingthe user of the kit to extract the appropriate nucleic acid sample, andanalyze the same according to the methods of the invention. The primersthat are provided with the kit will vary, depending upon the purpose ofthe kit and the DNA that is desired to be tested using the kit.

A kit can also be designed to detect a desired or variety of singlenucleotide polymorphisms, especially those associated with an undesiredcondition or disease. For example, one kit can comprise, among othercomponents, a set or sets of primers to amplify one or more loci ofinterest associated with breast cancer. Another kit can comprise, amongother components, a set or sets of primers for genes associated with apredisposition to develop type I or type II diabetes. Still, another kitcan comprise, among other components, a set or sets of primers for genesassociated with a predisposition to develop heart disease. Details ofutilities for such kits are provided in the “Utilities” section below.

Utilities

The methods of the invention can be used whenever it is desired to knowthe sequence of a certain nucleic acid, locus of interest or loci ofinterest therein. The method of the invention is especially useful whenapplied to genomic DNA. When DNA from an organism-specific orspecies-specific locus or loci of interest is amplified, the method ofthe invention can be used in genotyping for identification of the sourceof the DNA, and thus confirm or provide the identity of the organism orspecies from which the DNA sample was derived. The organism can be anynucleic acid containing organism, for example, virus, bacterium, yeast,plant, animal or human.

Within any population of organisms, the method of the invention isuseful to identify differences between the sequence of the samplenucleic acid and that of a known nucleic acid. Such differences caninclude, for example, allelic variations, mutations, polymorphisms andespecially single nucleotide polymorphisms.

In a preferred embodiment, the method of the invention provides a methodfor identification of single nucleotide polymorphisms.

In a preferred embodiment, the method of the invention provides a methodfor identification of the presence of a disease, especially a geneticdisease that arises as a result of the presence of a genomic sequence,or other biological condition that it is desired to identify in anindividual for which it is desired to know the same. The identificationof such sequence in the subject based on the presence of such genomicsequence can be used, for example, to determine if the subject is acarrier or to assess if the subject is predisposed to developing acertain genetic trait, condition or disease. The method of the inventionis especially useful in prenatal genetic testing of parents and child.Examples of some of the diseases that can be diagnosed by this inventionare listed in Table II.

TABLE II Achondroplasia Adrenoleukodysrophy, X-LinkedAgammaglobulinemia, X-Linked Alagille Syndrome Alpha-ThalassemiaX-Linked Mental Retardation Syndrome Alzheimer Disease AlzheimerDisease, Early-Onset Familial Amyotrophic Lateral Schlerosis OverviewAndrogen Insensitivity Syndrome Angelman Syndrome Ataxia Overview,Hereditary Ataxia-Telangiectasia Becker Muscular Dystrophy (also TheDystrophinopathies) Beckwith-Wiedemann Syndrome Beta-Thalassern iaBiotinidase Deficiency Branchiootorenal Syndrome BRCA1 and BRCA2Hereditary Breast/Ovarian Cancer Breast Cancer CADASIL Canavan DiseaseCancer Charcot-Marie-Tooth Hereditary Neuropathy Charcot-Marie-ToothNeuropathy Type 1 Charcot-Marie-Tooth Neuropathy Type 2Charcot-Marie-Tooth Neuropathy Type 4 Charcot-Marie-Tooth NeuropathyType X Cockayne Syndrome Colon Cancer Contractural Arachnodactyly,Congenital Craniosynostosis Syndromes (FGFR-Related) Cystic FibrosisCystinosis Deafness and Hereditary Hearing Loss DRPLA(Dentatorubral-Pallidoluysian Atrophy) DiGeorge Syndrome (also 22q11Deletion Syndrome) Dilated Cardiomyopathy, X-Linked Down Syndrome(Trisomy 21) Duchenne Muscular Dystrophy (also The Dystrophinopathies)Dystonia, Early-Onset Primary (DYT1) Dystrophinopathies, TheEhlers-Danlos Syndrome, Kyphoscoliotic Form Ehlers-Danlos Syndrome,Vascular Type Epidermolysis Bullosa Simplex Exostoses, HereditaryMultiple Facioscapulohumeral Muscular Dystrophy Factor V LeidenThrombophilia Familial Adenomatous Polyposis (FAP) FamilialMediterranean Fever Fragile X Syndrome Friedreich Ataxia FrontotemporalDemetia with Parkinsonism-17 Galactosemia Gaucher DiseaseHemochromatosis, Hereditary Hemophilia A Hemophilia B HemorrhagicTelangiectasia, Hereditary Hearing Loss and Deafness, Nonsyndromic,DFNA3 (Connexin 26) Hearing Loss and Deafness, Nonsyndromic, DFNB1(Connexin 26) Hereditary Spastic Paraplegia Herrnansky-Pudlak SyndromeHexosarn in idase A Deficiency (also Tay-Sachs) Huntington DiseaseHypochondroplasia Ichthyosis, Congenital, Autosomal RecessiveIncontinentia Pigmenti Kennedy Disease (also Spinal and Bulbar MuscularAtrophy) Krabbe Disease Leber Hereditary Optic Neuropathy Lesch-NyhanSyndrome Leukemias Li-Fraumeni Syndrome Limb-Girdle Muscular DystrophyLipoprotein Lipase Deficiency, Familial Lissencephaly Marfan SyndromeMELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-LikeEpisodes) Monosomies Multiple Endocrine Neoplasia Type 2 MultipleExostoses, Hereditary Muscular Dystrophy, Congenital Myotonic DystrophyNephrogenic Diabetes Insipidus Neurofibromatosis 1 Neurofibromatosis 2Neuropathy with Liability to Pressure Palsies, Hereditary Niemann-PickDisease Type C Nijmegen Breakage Syndrome Norrie Disease OculocutaneousAlbinism Type I Oculopharyngeal Muscular Dystrophy Ovarian CancerPallister-Hall Syndrome Parkin Type of Juvenile Parkinson DiseasePelizaeus-Merzbacher Disease Pendred Syndrome Peutz-Jeghers SyndromePhenylalanine Hydroxylase Deficiency Prader-Willi Syndrome PROP1-RelatedCombined Pituitary Hormone Deficiency (CPHD) Prostate Cancer RetinitisPigmentosa Retinoblastoma Rothmund-Thomson Syndrome Smith-Lemli-OpitzSyndrome Spastic Paraplegia, Hereditary Spinal and Bulbar MuscularAtrophy (also Kennedy Disease) Spinal Muscular Atrophy SpinocerebellarAtaxia Type 1 Spinocerebellar Ataxia Type 2 Spinocerebellar Ataxia Type3 Spinocerebellar Ataxia Type 6 Spinocerebellar Ataxia Type 7 SticklerSyndrome (Hereditary Arthroophthalmopathy) Tay-Sachs (also GM2Gangliosidoses) Trisomies Tuberous Sclerosis Complex Usher Syndrome TypeI Usher Syndrome Type II Velocardiofacial Syndrome (also 22q11 DeletionSyndrome) Von Hippel-Lindau Syndrome Williams Syndrome Wilson DiseaseX-Linked Adrenoleukodystrophy X-Linked Agammaglobulinemia X-LinkedDilated Cardiomyopathy (also The Dystrophinopathies) X-Linked HypotonicFacies Mental Retardation Syndrome

The method of the invention is useful for screening an individual atmultiple loci of interest, such as tens, hundreds, or even thousands ofloci of interest associated with a genetic trait or genetic disease bysequencing the loci of interest that are associated with the trait ordisease state, especially those most frequently associated with suchtrait or condition. The invention is useful for analyzing a particularset of diseases including but not limited to heart disease, cancer,endocrine disorders, immune disorders, neurological disorders,musculoskeletal disorders, ophthalmologic disorders, geneticabnormalities, trisomies, monosomies, transversions, translocations,skin disorders, and familial diseases.

The method of the invention can be used to genotype microorganisms so asto rapidly identify the presence of a specific microorganism in asubstance, for example, a food substance. In that regard, the method ofthe invention provides a rapid way to analyze food, liquids or airsamples for the presence of an undesired biological contamination, forexample, microbiological, fungal or animal waste material. The inventionis useful for detecting a variety of organisms, including but notlimited to bacteria, viruses, fungi, protozoa, molds, yeasts, plants,animals, and archeabacteria. The invention is useful for detectingorganisms collected from a variety of sources including but not limitedto water, air, hotels, conference rooms, swimming pools, bathrooms,aircraft, spacecraft, trains, buses, cars, offices, homes, businesses,churches, parks, beaches, athletic facilities, amusement parks,theaters, and any other facility that is a meeting place for the public.

The method of the invention can be used to test for the presence of manytypes of bacteria or viruses in blood cultures from human or animalblood samples.

The method of the invention can also be used to confirm or identify thepresence of a desired or undesired yeast strain, or certain traitsthereof, in fermentation products, e.g. wine, beer, and other alcoholsor to identify the absence thereof.

The method of the invention can also be used to confirm or identify therelationship of a DNA of unknown sequence to a DNA of known origin orsequence, for example, for use in criminology, forensic science,maternity or paternity testing, archaeological analysis, and the like.

The method the invention can also be used to determine the genotypes ofplants, trees and bushes, and hybrid plants, trees and bushes, includingplants, trees and bushes that produce fruits and vegetables and othercrops, including but not limited to wheat, barley, corn, tobacco,alfalfa, apples, apricots, bananas, oranges, pears, nectarines, figs,dates, raisins, plums, peaches, apricots, blueberries, strawberries,cranberries, berries, cherries, kiwis, limes, lemons, melons,pineapples, plantains, guavas, prunes, passion fruit, tangerines,grapefruit, grapes, watermelon, cantelope, honeydew melons,pomegranates, persimmons, nuts, artichokes, bean sprouts, beets,cardoon, chayote, endive, leeks, okra, green onions, scallions,shallots, parsnips, sweet potatoes, yams, asparagus, avocados, kohlrabi,rutabaga, eggplant, squash, turnips, pumpkins, tomatoes, potatoes,cucumbers, carrots, cabbage, celery, broccoli, cauliflower, radishes,peppers, spinach, mushrooms, zucchini, onions, peas, beans, and otherlegumes.

Especially, the method of the invention is useful to screen a mixture ofnucleic acid samples that contain many different loci of interest and/ora mixture of nucleic acid samples from different sources that are to beanalyzed for a locus of interest. Examples of large scale screeninginclude taking samples of nucleic acid from herds of farm animals, orcrops of food plants such as, for example, corn or wheat, pooling thesame, and then later analyzing the pooled samples for the presence of anundesired genetic marker, with individual samples only being analyzed ata later date if the pooled sample indicates the presence of suchundesired genetic sequence. An example of an undesired genetic sequencewould be the detection of viral or bacterial nucleic acid sequence inthe nucleic acid samples taken from the farm animals, for example,mycobacterium or hoof and mouth disease virus sequences or fungal orbacterial pathogen of plants.

Another example where pools of nucleic acid can be used is to test forthe presence of a pathogen or gene mutation in samples from one or moretissues from an animal or human subject, living or dead, especially asubject who can be in need of treatment if the pathogen or mutation isdetected. For example, numerous samples can be taken from an animal orhuman subject to be screened for the presence of a pathogen or otherwiseundesired genetic mutation, the loci of interest from each biologicalsample amplified individually, and then samples of the amplified DNAcombined for the restriction digestion, “filling in,” and detection.This would be useful as an initial screening for the assay of thepresence or absence of nucleic acid sequences that would be diagnosticof the presence of a pathogen or mutation. Then, if the undesirednucleic acid sequence of the pathogen or mutation was detected, theindividual samples could be separately analyzed to determine thedistribution of the undesired sequence. Such an analysis is especiallycost effective when there are large numbers of samples to be assayed.Samples of pathogens include the mycobacteria, especially those thatcause tuberculosis or paratuberculosis, bacteria, especially bacterialpathogens used in biological warfare, including Bacillus anthracis, andvirulent bacteria capable of causing food poisoning, viruses, especiallythe influenza and AIDS virus, and mutations known to be associated withmalignant cells. Such an analysis would also be advantageous for thelarge scale screening of food products for pathogenic bacteria.

Conversely, the method of the invention can be used to detect thepresence and distribution of a desired genetic sequence at variouslocations in a plant, animal or human subject, or in a population ofsubjects, e.g. by screening of a combined sample followed by screeningof individual samples, as necessary.

The method of the invention is useful for analyzing genetic variationsof an individual that have an effect on drug metabolism, druginteractions, and the responsiveness to a drug or to multiple drugs. Themethod of the invention is especially useful in pharmacogenomics.

Having now generally described the invention, the same will becomebetter understood by reference to certain specific examples which areincluded herein for purposes of illustration only and are not intendedto be limiting unless other wise specified.

EXAMPLES

The following examples are illustrative only and are not intended tolimit the scope of the invention as defined by the claims.

Example 1

DNA sequences were amplified by PCR, wherein the annealing step in cycle1 was performed at a specified temperature, and then increased in cycle2, and further increased in cycle 3 for the purpose of reducingnon-specific amplification. The TM1 of cycle 1 of PCR was determined bycalculating the melting temperature of the 3′ region, which anneals tothe template DNA, of the second primer. For example, in FIG. 1B, the TM1can be about the melting temperature of region “c.” The annealingtemperature was raised in cycle 2, to TM2, which was about the meltingtemperature of the 3′ region, which anneals to the template DNA, of thefirst primer. For example, in FIG. 1C, the annealing temperature (TM2)corresponds to the melting temperature of region “b′”. In cycle 3, theannealing temperature was raised to TM3, which was about the meltingtemperature of the entire sequence of the second primer For example, inFIG. 1D, the annealing temperature (TM3) corresponds to the meltingtemperature of region “c”+region “d”. The remaining cycles ofamplification were performed at TM3.

Preparation of Template DNA

The template DNA was prepared from a 5 ml sample of blood obtained byvenipuncture from a human volunteer with informed consent. Blood wascollected from 36 volunteers. Template DNA was isolated from each bloodsample using QIAamp DNA Blood Midi Kit supplied by QIAGEN (Catalognumber 51183). Following isolation, the template DNA from each of the 36volunteers was pooled for further analysis.

Design of Primers

The following four single nucleotide polymorphisms were analyzed: SNPHC21S00340, identification number as assigned by Human Chromosome 21cSNP Database, (FIG. 3, lane 1) located on chromosome 21; SNP TSC0095512 (FIG. 3, lane 2) located on chromosome 1, SNP TSC 0214366 (FIG.3, lane 3) located on chromosome 1; and SNP TSC 0087315 (FIG. 3, lane 4)located on chromosome 1. The SNP Consortium Ltd database can be accessedat http://snp.cshl.org/, website address effective as of Feb. 14, 2002.

SNP HC21S00340 was amplified using the following primers:

First primer: 5′ TAGAATAGCACTGAATTCAGGAATACAATCATTGTCAC 3′ (SEQ ID NO:9)Second primer: 5′ ATCACGATAAACGGCCAAACTCAGGTTA 3′ (SEQ ID NO:10)

SNP TSC0095512 was amplified using the following primers:

First primer: 5′ AAGTTTAGATCAGAATTCGTGAAAGCAGAAGTTGTCTG 3′ (SEQ IDNO:11) Second primer: 5′ TCTCCAACTAACGGCTCATCGAGTAAAG 3′ (SEQ ID NO:12)

SNP TSC0214366 was amplified using the following primers:

First primer: 5′ ATGACTAGCTATGAATTCGTTCAAGGTAGAAAATGGAA 3′ (SEQ IDNO:13) Second primer: 5′ GAGAATTAGAACGGCCCAAATCCCACTC 3′ (SEQ ID NO:16)

SNP TSC 0087315 was amplified using the following primers:

First primer: 5′ TTACAATGCATGAATTCATCTTGGTCTCTCAAAGTGC 3′ (SEQ ID NO:15)Second primer: 5′ TGGACCATAAACGGCCAAAAACTGTAAG 3′ (SEQ ID NO:16)

All primers were designed such that the 3′ region was complementary toeither the upstream or downstream sequence flanking each locus ofinterest and the 5′ region contained a restriction enzyme recognitionsite. The first primer contained a biotin tag at the 5′ end and arecognition site for the restriction enzyme EcoRI. The second primercontained the recognition site for the restriction enzyme BceA I.

PCR Reaction

All four loci of interest were amplified from the template genomic DNAusing PCR (U.S. Pat. Nos. 4,683,195 and 4,683,202). The components ofthe PCR reaction were as follows: 40 ng of template DNA, 5 μM firstprimer, 5 μM second primer, 1× HotStarTaq Master Mix as obtained fromQiagen (Catalog No. 203443). The HotStarTaq Master Mix contained DNApolymerase, PCR buffer, 200 μM of each dNTP, and 1.5 mM MgCl₂.

Amplification of each template DNA that contained the SNP of interestwas performed using three different series of annealing temperatures,herein referred to as low stringency annealing temperature, mediumstringency annealing temperature, and high stringency annealingtemperature. Regardless of the annealing temperature protocol, each PCRreaction consisted of 40 cycles of amplification. PCR reactions wereperformed using the HotStarTaq Master Mix Kit supplied by QIAGEN. Asinstructed by the manufacturer, the reactions were incubated at 95° C.for 15 min. prior to the first cycle of PCR. The denaturation step aftereach extension step was performed at 95° C. for 30 sec. The annealingreaction was performed at a temperature that permitted efficientextension without any increase in temperature.

The low stringency annealing reaction comprised three differentannealing temperatures in each of the first three cycles. The annealingtemperature for the first cycle was 37° C. for 30 sec.; the annealingtemperature for the second cycle was 57° C. for 30 sec.; the annealingtemperature for the third cycle was 64° C. for 30 sec. Annealing wasperformed at 64° C. for subsequent cycles until completion.

As shown in the photograph of the gel (FIG. 3A), multiple bands wereobserved after amplification of SNP TSC 0087315 (lane 4). Amplificationof SNP HC21S00340 (lane 1), SNP TSC0095512 (lane 2), and SNP TSC0214366(lane 3) generated a single band of high intensity and one band of faintintensity, which was of higher molecular weight. When the low annealingtemperature conditions were used, the correct size product was generatedand this was the predominant product in each reaction.

The medium stringency annealing reaction comprised three differentannealing temperatures in each of the first three cycles. The annealingtemperature for the first cycle was 40° C. for 30 seconds; the annealingtemperature for the second cycle was 60° C. for 30 seconds; and theannealing temperature for the third cycle was 67° C. for 30 seconds.Annealing was performed at 67° C. for subsequent cycles untilcompletion. Similar to what was observed under low stringency annealingconditions, amplification of SNP TSC0087315 (FIG. 3B, lane 4) generatedmultiple bands under conditions of medium stringency. Amplification ofthe other three SNPs (lanes 1-3) produced a single band. These resultsdemonstrate that variable annealing temperatures can be used to cleanlyamplify loci of interest from genomic DNA with a primer that has anannealing length of 13 bases.

The high stringency annealing reaction was comprised of three differentannealing temperatures in each of the first three cycles. The annealingtemperature of the first cycle was 46° C. for 30 seconds; the annealingtemperature of the second cycle was 65° C. for 30 seconds; and theannealing temperature for the third cycle was 72° C. for 30 seconds.Annealing was performed at 72° C. for subsequent cycles untilcompletion. As shown in the photograph of the gel (FIG. 3C),amplification of SNP TSC0087315 (lane 4) using the high stringencyannealing temperatures generated a single band of the correct molecularweight. By raising the annealing temperatures for each of the firstthree cycles, non-specific amplification was eliminated. Amplificationof SNP TSC0095512 (lane 2) generated a single band. SNPs HC21S00340(lane 1), and TSC0214366 (lane 3) failed to amplify at the highstringency annealing temperatures, however, at the medium stringencyannealing temperatures, these SNPs amplified as a single band. Theseresults demonstrate that variable annealing temperatures can be used toreduce non-specific PCR products, as demonstrated for SNP TSC0087315(FIG. 3, lane 4).

Example 2

SNPs on chromosomes 1 (TSC0095512), 13 (TSC0264580), and 21 (HC21S00027)were analyzed. SNP TSC0095512 was analyzed using two different sets ofprimers, and SNP HC21S00027 was analyzed using two types of reactionsfor the incorporation of nucleotides.

Preparation of Template DNA

The template DNA was prepared from a 5 ml sample of blood obtained byvenipuncture from a human volunteer with informed consent. Template DNAwas isolated using the QIAmp DNA Blood Midi Kit supplied by QIAGEN(Catalog number 51183). The template DNA was isolated as perinstructions included in the kit. Following isolation, template DNA fromthirty-six human volunteers were pooled together and cut with therestriction enzyme EcoRI. The restriction enzyme digestion was performedas per manufacturer's instructions.

Design of Primers

SNP HC21S00027 was amplified by PCR using the following primer set:

First primer: 5′ ATAACCGTATGCGAATTCTATAATTTTCCTGATAAAGG 3′ (SEQ IDNO:17) Second primer: 5′ CTTAAATCAGGGGACTAGGTAAACTTCA 3′ (SEQ ID NO:18)

The first primer contained a biotin tag at the extreme 5′ end, and thenucleotide sequence for the restriction enzyme EcoRI. The second primercontained the nucleotide sequence for the restriction enzyme BsmF I(FIG. 4A).

Also, SNP HC21S00027 was amplified by PCR using the same first primerbut a different second primer with the following sequence:

Second primer: 5′ CTTAAATCAGACGGCTAGGTAAACTTCA 3′ (SEQ ID NO:19)

This second primer contained the recognition site for the restrictionenzyme BceA I (FIG. 4B).

SNP TSC0095512 was amplified by PCR using the following primers:

First primer: 5′ AAGTTTAGATCAGAATTCGTGAAAGCAGAAGTTGTCTG 3′ (SEQ IDNO:11) Second primer: 5′ TCTCCAACTAGGGACTCATCGAGTAAAG 3′ (SEQ ID NO:20)

The first primer had a biotin tag at the 5′ end and contained arestriction enzyme recognition site for EcoRI. The second primercontained a restriction enzyme recognition site for BsmF I (FIG. 4C).

Also, SNP TSC0095512 was amplified using the same first primer and adifferent second primer with the following sequence:

Second primer: 5′ TCTCCAACTAACGGCTCATCGAGTAAAG 3′ (SEQ ID NO:12)

This second primer contained the recognition site for the restrictionenzyme BceA I (FIG. 4D).

SNP TSC0264580, which is located on chromosome 13, was amplified withthe following primers:

First primer: 5′ AACGCCGGGCGAGAATTCAGTTTTTCAACTTGCAAGG 3′ (SEQ ID NO:21)

Second primer: 5′ CTACACATATCTGGGACGTTGGCCATCC 3′ (SEQ ID NO:22)

The first primer contained a biotin tag at the extreme 5′ end and had arestriction enzyme recognition site for EcoRI. The second primercontained a restriction enzyme recognition site for BsmF I.

PCR Reaction

All loci of interest were amplified from the template genomic DNA usingthe polymerase chain reaction (PCR, U.S. Pat. Nos. 4,683,195 and4,683,202, incorporated herein by reference). In this example, the lociof interest were amplified in separate reaction tubes but they couldalso be amplified together in a single PCR reaction. For increasedspecificity, a “hot-start” PCR was used. PCR reactions were performedusing the HotStarTaq Master Mix Kit supplied by QIAGEN (catalog number203443). The amount of template DNA and primer per reaction can beoptimized for each locus of interest but in this example, 40 ng oftemplate human genomic DNA and 5 μM of each primer were used. Fortycycles of PCR were performed. The following PCR conditions were used:

-   -   (1) 95° C. for 15 minutes and 15 seconds;    -   (2) 37° C. for 30 seconds;    -   (3) 95° C. for 30 seconds;    -   (4) 57° C. for 30 seconds;    -   (5) 95° C. for 30 seconds;    -   (6) 64° C. for 30 seconds;    -   (7) 95° C. for 30 seconds;    -   (8) Repeat steps 6 and 7 thirty nine (39) times;    -   (9) 72° C. for 5 minutes.

In the first cycle of PCR, the annealing temperature was about themelting temperature of the 3′ annealing region of the second primers,which was 37° C. The annealing temperature in the second cycle of PCRwas about the melting temperature of the 3′ region, which anneals to thetemplate DNA, of the first primer, which was 57° C. The annealingtemperature in the third cycle of PCR was about the melting temperatureof the entire sequence of the second primer, which was 64° C. Theannealing temperature for the remaining cycles was 64° C. Escalating theannealing temperature from TM1 to TM2 to TM3 in the first three cyclesof PCR greatly improves specificity. These annealing temperatures arerepresentative, and the skilled artisan will understand the annealingtemperatures for each cycle are dependent on the specific primers used.

The temperatures and times for denaturing, annealing, and extension, canbe optimized by trying various settings and using the parameters thatyield the best results. Schematics of the PCR products for SNPHC21S00027 and SNP TSC0095512 are shown in FIGS. 5A-5D.

Purification of Fragment of Interest

The PCR products were separated from the genomic template DNA. Each PCRproduct was divided into four separate reaction wells of a Streptawell,transparent, High-Bind plate from Roche Diagnostics GmbH (catalog number1 645 692, as listed in Roche Molecular Biochemicals, 2001 BiochemicalsCatalog). The first primers contained a 5′ biotin tag so the PCRproducts bound to the Streptavidin coated wells while the genomictemplate DNA did not. The streptavidin binding reaction was performedusing a Thermomixer (Eppendorf) at 1000 rpm for 20 min. at 37° C. Eachwell was aspirated to remove unbound material, and washed three timeswith 1×PBS, with gentle mixing (Kandpal et al., Nucl. Acids Res.18:1789-1795 (1990); Kaneoka et al., Biotechniques 10:30-34 (1991);Green et al., Nucl. Acids Res. 18:6163-6164 (1990)).

Restriction Enzyme Digestion of Isolated Fragments

The purified PCR products were digested with the restriction enzyme thatbound the recognition site incorporated into the PCR products from thesecond primer. SNP HC21S00027 (FIGS. 6A and 6B) and SNP TSC0095512(FIGS. 6C and 6D) were amplified in separate reactions using twodifferent second primers. FIG. 6A (SNP HC21S00027) and FIG. 6C (SNPTSC0095512) depict the PCR products after digestion with the restrictionenzyme BsmF I (New England Biolabs catalog number R0572S). FIG. 6B (SNPHC21S00027) and FIG. 6D (SNP TSC0095512) depict the PCR products afterdigestion with the restriction enzyme BceA I (New England Biolabs,catalog number R0623S). The digests were performed in the Streptawellsfollowing the instructions supplied with the restriction enzyme. SNPTSC0264580 was digested with BsmF I. After digestion with theappropriate restriction enzyme, the wells were washed three times withPBS to remove the cleaved fragments.

Incorporation of Labeled Nucleotide

The restriction enzyme digest described above yielded a DNA fragmentwith a 5′ overhang, which contained the SNP site or locus of interestand a 3′ recessed end. The 5′ overhang functioned as a template allowingincorporation of a nucleotide or nucleotides in the presence of a DNApolymerase.

For each SNP, four separate fill in reactions were performed; each ofthe four reactions contained a different fluorescently labeled ddNTP(ddATP, ddTTP, ddGTP, or ddCTP). The following components were added toeach fill in reaction: 1 μl of a fluorescently labeled ddNTP, 0.5 μl ofunlabeled ddNTPs (40 μM), which contained all nucleotides except thenucleotide that was fluorescently labeled, 2 μl of 10× sequenase buffer,0.25 μl of Sequenase, and water as needed for a 20 μl reaction. All ofthe fill in reactions were performed at 40° C. for 10 min.Non-fluorescently labeled ddNTP was purchased from Fermentas Inc.(Hanover, Md.). All other labeling reagents were obtained from Amersham(Thermo Sequenase Dye Terminator Cycle Sequencing Core Kit, US 79565).In the presence of fluorescently labeled ddNTPs, the 3′ recessed end wasextended by one base, which corresponds to the SNP or locus of interest(FIGS. 7A-7D).

A mixture of labeled ddNTPs and unlabeled dNTPs also was used for the“fill in” reaction for SNP HC21S00027. The “fill in” conditions were asdescribed above except that a mixture containing 40 μM unlabeled dNTPs,1 μl fluorescently labeled ddATP, 1 μl fluorescently labeled ddTTP, 1 μlfluorescently labeled ddCTP, and 1 μl ddGTP was used. The fluorescentddNTPs were obtained from Amersham (Thermo Sequenase Dye TerminatorCycle Sequencing Core Kit, US 79565; Amersham did not publish theconcentrations of the fluorescent nucleotides). SNP HC21S00027 wasdigested with the restriction enzyme BsmF I, which generated a 5′overhang of four bases. As shown in FIG. 7E, if the first nucleotideincorporated is a labeled ddNTP, the 3′ recessed end is filled in by onebase, allowing detection of the SNP or locus of interest. However, ifthe first nucleotide incorporated is a dNTP, the polymerase continues toincorporate nucleotides until a ddNTP is filled in. For example, thefirst two nucleotides may be filled in with dNTPs, and the thirdnucleotide with a ddNTP, allowing detection of the third nucleotide inthe overhang. Thus, the sequence of the entire 5′ overhang may bedetermined, which increases the information obtained from each SNP orlocus of interest.

After labeling, each Streptawell was rinsed with 1×PBS (100 μl) threetimes. The “filled in” DNA fragments were then released from theStreptawells by digestion with the restriction enzyme EcoRI, accordingto the manufacturer's instructions that were supplied with the enzyme(FIGS. 8A-8D). Digestion was performed for 1 hour at 37° C. with shakingat 120 rpm.

Detection of the Locus of Interest

After release from the streptavidin matrix, 2-3 μl of the 10 μl samplewas loaded in a 48 well membrane tray (The Gel Company, catalog numberTAM48-01). The sample in the tray was absorbed with a 48 Flow MembraneComb (The Gel Company, catalog number AM48), and inserted into a 36 cm5% acrylamide (urea) gel (BioWhittaker Molecular Applications, LongRanger Run Gel Packs, catalog number 50691).

The sample was electrophoresed into the gel at 3000 volts for 3 min. Themembrane comb was removed, and the gel was run for 3 hours on an ABI 377Automated Sequencing Machine. The incorporated labeled nucleotide wasdetected by fluorescence.

As shown in FIG. 9A, from a sample of thirty six (36) individuals, oneof two nucleotides, either adenosine or guanine, was detected at SNPHC21S00027. These are the two nucleotides reported to exist at SNPHC21S00027 (http://snp.cshl.org/snpsearch.shtml).

One of two nucleotides, either guanine or cytosine, was detected at SNPTSC0095512 (FIG. 9B). The same results were obtained whether the locusof interest was amplified with a second primer that contained arecognition site for BceA I or the second primer contained a recognitionsite for BsmF I.

As shown in FIG. 9C, one of two nucleotides was detected at SNPTSC0264580, which was either adenosine or cytosine. These are the twonucleotides reported for this SNP site(http://snp.cshl.org/snpsearch.shtml). In addition, a thymidine wasdetected one base upstream of the locus of interest. In a sequencedependent manner, BsmF I cuts some DNA molecules at the 10/14 positionand other DNA molecules, which have the same sequence, at the 11/15position. When the restriction enzyme BsmF I cuts 11 nucleotides away onthe sense strand and 15 nucleotides away on the antisense strand, the 3′recessed end is one base upstream of the SNP site. The sequence of SNPTSC0264580 indicated that the base immediately preceding the SNP sitewas a thymidine. The incorporation of a labeled ddNTP into this positiongenerated a fragment one base smaller than the fragment that was cut atthe 10/14 position. Thus, the DNA molecules cut at the 11/15 positionprovided sequence information about the base immediately preceding theSNP site, and the DNA molecules cut at the 10/14 position providedsequence information about the SNP site.

SNP HC21S00027 was amplified using a second primer that contained therecognition site for BsmF I. A mixture of labeled ddNTPs and unlabeleddNTPs was used to fill in the 5′ overhang generated by digestion withBsmF I. If a dNTP was incorporated, the polymerase continued toincorporate nucleotides until a ddNTP was incorporated. A population ofDNA fragments, each differing by one base, was generated, which allowedthe full sequence of the overhang to be determined.

As seen in FIG. 9D, an adenosine was detected, which was complementaryto the nucleotide (a thymidine) immediately preceding the SNP or locusof interest. This nucleotide was detected because of the 11/15 cuttingproperty of BsmF I, which is described in detail above. A guanine and anadenosine were detected at the SNP site, which are the two nucleotidesreported for this SNP site (FIG. 9A). The two nucleotides were detectedat the SNP site because the molecular weights of the dyes differ, whichallowed separation of the two nucleotides. The next nucleotide detectedwas a thymidine, which is complementary to the nucleotide immediatelydownstream of the SNP site. The next nucleotide detected was a guanine,which was complementary to the nucleotide two bases downstream of theSNP site. Finally, an adenosine was detected, which was complementary tothe third nucleotide downstream of the SNP site. Sequence informationwas obtained not only for the SNP site but for the nucleotideimmediately preceding the SNP site and the next three nucleotides.

None of the loci of interest contained a mutation. However, if one ofthe loci of interest harbored a mutation including but not limited to apoint mutation, insertion, deletion, translocation or any combination ofsaid mutations, it could be identified by comparison to the consensus orpublished sequence. Comparison of the sequences attributed to each ofthe loci of interest to the native, non-disease related sequence of thegene at each locus of interest determines the presence or absence of amutation in that sequence. The finding of a mutation in the sequence isthen interpreted as the presence of the indicated disease, or apredisposition to develop the same, as appropriate, in that individual.The relative amounts of the mutated vs. normal or non-mutated sequencecan be assessed to determine if the subject has one or two alleles ofthe mutated sequence, and thus whether the subject is a carrier, orwhether the indicated mutation results in a dominant or recessivecondition.

Example 3

Four loci of interest from chromosome 1 and two loci of interest fromchromosome 21 were amplified in separate PCR reactions, pooled together,and analyzed. The primers were designed so that each amplified locus ofinterest was a different size, which allowed detection of the loci ofinterest.

Preparation of Template DNA

The template DNA was prepared from a 5 ml sample of blood obtained byvenipuncture from a human volunteer with informed consent. Template DNAwas isolated using the QIAmp DNA Blood Midi Kit supplied by QIAGEN(Catalog number 51183). The template DNA was isolated as perinstructions included in the kit. Template DNA was isolated fromthirty-six human volunteers, and then pooled into a single sample forfurther analysis.

Design of Primers

SNP TSC 0087315 was amplified using the following primers:

First primer: 5′ TTACAATGCATGAATTCATCTTGGTCTCTCAAAGTGC 3′ (SEQ ID NO:15)Second primer: 5′ TGGACCATAAACGGCCAAAAACTGTAAG 3′ (SEQ ID NO:16)

SNP TSC0214366 was amplified using the following primers:

First primer: 5′ ATGACTAGCTATGAATTCGTTCAAGGTAGAAAATGGAA 3′ (SEQ IDNO:13) Second primer: 5′ GAGAATTAGAACGGCCCAAATCCCACTC 3′ (SEQ ID NO:14)

SNP TSC 0413944 was amplified with the following primers:

First primer: 5′ TACCTTTTGATCGAATTCAAGGCCAAAAATATTAAGTT 3′ (SEQ IDNO:23) Second primer: 5′ TCGAACTTTAACGGCCTTAGAGTAGAGA 3′ (SEQ ID NO:24)

SNP TSC0095512 was amplified using the following primers:

First primer: 5′ AAGTTTAGATCAGAATTCGTGAAAGCAGAAGTTGTCTG 3′ (SEQ IDNO:11) Second primer: 5′ TCTCCAACTAACGGCTCATCGAGTAAAG 3′ (SEQ ID NO:12)

SNP HC21S00131 was amplified with the following primers:

First primer: 5′ CGATTTCGATAAGAATTCAAAAGCAGTTCTTAGTTCAG 3′ (SEQ IDNO:25) Second primer: 5′ TGCGAATCTTACGGCTGCATCACATTCA 3′ (SEQ ID NO:26)

SNP HC21S00027 was amplified with the following primers:

First primer: 5′ ATAACCGTATGCGAATTCTATAATTTTCCTGATAAAGG 3′ (SEQ IDNO:17) Second primer: 5′ CTTAAATCAGACGGCTAGGTAAACTTCA 3′ (SEQ ID NO:19)

For each SNP, the first primer contained a recognition site for therestriction enzyme EcoRI and had a biotin tag at the extreme 5′ end. Thesecond primer used to amplify each SNP contained a recognition site forthe restriction enzyme BceA I.

PCR Reaction

The PCR reactions were performed as described in Example 2 except thatthe following annealing temperatures were used: the annealingtemperature for the first cycle of PCR was 37° C. for 30 seconds, theannealing temperature for the second cycle of PCR was 57° C. for 30seconds, and the annealing temperature for the third cycle of PCR was64° C. for 30 seconds. All subsequent cycles had an annealingtemperature of 64° C. for 30 seconds. Thirty seven (37) cycles of PCRwere performed. After PCR, ¼ of the volume was removed from eachreaction, and combined into a single tube.

Purification of Fragment of Interest

The PCR products (now combined into one sample, and referred to as “thesample”) were separated from the genomic template DNA as described inExample 2 except that the sample was bound to a single well of aStreptawell microtiter plate.

Restriction Enzyme Digestion of Isolated Fragments

The sample was digested with the restriction enzyme BceA I, which boundthe recognition site in the second primer. The restriction enzymedigestions were performed following the instructions supplied with theenzyme. After the restriction enzyme digest, the wells were washed threetimes with 1×PBS.

Incorporation of Nucleotides

The restriction enzyme digest described above yielded DNA molecules witha 5′ overhang, which contained the SNP site or locus of interest and a3′ recessed end. The 5′ overhang functioned as a template allowingincorporation of a nucleotide in the presence of a DNA polymerase.

The following components were used for the fill in reaction: 1 μl offluorescently labeled ddATP; 1 μl of fluorescently labeled ddTTP; 1 μlof fluorescently labeled ddGTP; 1 μl of fluorescently labeled ddCTP; 2μl of 10× sequenase buffer, 0.25 μl of Sequenase, and water as neededfor a 20 μl reaction. The fill in reaction was performed at 40° C. for10 min. All labeling reagents were obtained from Amersham (ThermoSequenase Dye Terminator Cycle Sequencing Core Kit (US 79565); theconcentration of the ddNTPS provided in the kit is proprietary and notpublished by Amersham). In the presence of fluorescently labeled ddNTPs,the 3′ recessed end was filled in by one base, which corresponds to theSNP or locus of interest.

After the incorporation of nucleotide, the Streptawell was rinsed with1×PBS (100 μl) three times. The “filled in” DNA fragments were thenreleased from the Streptawell by digestion with the restriction enzymeEcoRI following the manufacturer's instructions. Digestion was performedfor 1 hour at 37° C. with shaking at 120 rpm.

Detection of the Locus of Interest

After release from the streptavidin matrix, 2-3 μl of the 10 μl samplewas loaded in a 48 well membrane tray (The Gel Company, catalog numberTAM48-01). The sample in the tray was absorbed with a 48 Flow MembraneComb (The Gel Company, catalog number AM48), and inserted into a 36 cm5% acrylamide (urea) gel (BioWhittaker Molecular Applications, LongRanger Run Gel Packs, catalog number 50691).

The sample was electrophoresed into the gel at 3000 volts for 3 min. Themembrane comb was removed, and the gel was run for 3 hours on an ABI 377Automated Sequencing Machine. The incorporated nucleotide was detectedby fluorescence.

The primers were designed so that each amplified locus of interestdiffered in size. As shown in FIG. 10, each amplified loci of interestdiffered by about 5-10 nucleotides, which allowed the loci of interestto be separated from one another by gel electrophoresis. Two nucleotideswere detected for SNP TSC0087315, which were guanine and cytosine. Theseare the two nucleotides reported to exist at SNP TSC0087315(http://snp.cshl.org/snpsearch.shtml). The sample comprised template DNAfrom 36 individuals and because the DNA molecules that incorporated aguanine differed in molecular weight from those that incorporated acytosine, distinct bands were seen for each nucleotide.

Two nucleotides were detected at SNP HC21S00027, which were guanine andadenosine (FIG. 10). The two nucleotides reported for this SNP site areguanine and adenosine (http://snp.cshl.org/snpsearch.shtml). Asdiscussed above, the sample contained template DNA from thirty-sixindividuals, and one would expect both nucleotides to be represented inthe sample. The molecular weight of the DNA fragments that incorporateda guanine was distinct from the DNA fragments that incorporated anadenosine, which allowed both nucleotides to be detected.

The nucleotide cytosine was detected at SNP TSC0214366 (FIG. 10). Thetwo nucleotides reported to exist at this SNP position are thymidine andcytosine.

The nucleotide guanine was detected at SNP TSC0413944 (FIG. 10). The twonucleotides reported for this SNP are guanine and cytosine(http://snp.cshl.org/snpsearch.shtml).

The nucleotide cytosine was detected at SNP TSC0095512 (FIG. 10). Thetwo nucleotides reported for this SNP site are guanine and cytosine(http://snp.cshl.org/snpsearch.shtml).

The nucleotide detected at SNP HC21S00131 was guanine. The twonucleotides reported for this SNP site are guanine and adenosine(http://snp.cshl.org/snpsearch.shtml).

As discussed above, the sample was comprised of DNA templates fromthirty-six individuals and one would expect both nucleotides at the SNPsites to be represented. For SNP TSC0413944, TSC0095512, TSC0214366 andHC21S00131, one of the two nucleotides was detected. It is likely thatboth nucleotides reported for these SNP sites are present in the samplebut that one fluorescent dye overwhelms the other. The molecular weightof the DNA molecules that incorporated one nucleotide did not allowefficient separation of the DNA molecules that incorporated the othernucleotide. However, the SNPs were readily separated from one another,and for each SNP, a proper nucleotide was incorporated. The sequences ofmultiple loci of interest from multiple chromosomes, which were treatedas a single sample after PCR, were determined.

A single reaction containing fluorescently labeled ddNTPs was performedwith the sample that contained multiple loci of interest. Alternatively,four separate fill in reactions can be performed where each reactioncontains one fluorescently labeled nucleotide (ddATP, ddTTP, ddGTP, orddCTP) and unlabeled ddNTPs (see Example 2, FIGS. 7A-7D and FIGS. 9A-C).Four separate “fill in” reactions will allow detection of any nucleotidethat is present at the loci of interest. For example, if analyzing asample that contains multiple loci of interest from a single individual,and said individual is heterozygous at one or more than one loci ofinterest, four separate “fill in” reactions can be used to determine thenucleotides at the heterozygous loci of interest.

Also, when analyzing a sample that contains templates from multipleindividuals, four separate “fill in” reactions will allow detection ofnucleotides present in the sample, independent of how frequent thenucleotide is found at the locus of interest. For example, if a samplecontains DNA templates from 50 individuals, and 49 of the individualshave a thymidine at the locus of interest, and one individual has aguanine, the performance of four separate “fill in” reactions, whereineach “fill in” reaction is run in a separate lane of a gel, such as inFIGS. 9A-9C, will allow detection of the guanine. When analyzing asample comprised of multiple DNA templates, multiple “fill in” reactionswill alleviate the need to distinguish multiple nucleotides at a singlesite of interest by differences in mass.

In this example, multiple single nucleotide polymorphisms were analyzed.It is also possible to determine the presence or absence of mutations,including point mutations, transitions, transversions, translocations,insertions, and deletions from multiple loci of interest. The multipleloci of interest can be from a single chromosome or from multiplechromosomes. The multiple loci of interest can be from a single gene orfrom multiple genes.

The sequence of multiple loci of interest that cause or predispose to adisease phenotype can be determined For example, one could amplify oneto tens to hundreds to thousands of genes implicated in cancer or anyother disease. The primers can be designed so that each amplified lociof interest differs in size. After PCR, the amplified loci of interestcan be combined and treated as a single sample. Alternatively, themultiple loci of interest can be amplified in one PCR reaction or thetotal number of loci of interest, for example 100, can be divided intosamples, for example 10 loci of interest per PCR reaction, and thenlater pooled. As demonstrated herein, the sequence of multiple loci ofinterest can be determined. Thus, in one reaction, the sequence of oneto ten to hundreds to thousands of genes that predispose or cause adisease phenotype can be determined.

Having now fully described the invention, the same will be understood bythose with skill in the art that the scope can be performed with a wideand equivalent range of conditions, parameters, and the like, withoutaffecting the spirit or scope of the invention or any embodimentthereof.

All documents, e.g., scientific publications, patents and patentpublications recited herein are hereby incorporated by reference intheir entirety to the same extent as if each individual document wasspecifically and individually indicated to be incorporated by referencein its entirety. Where the document cited only provides the first pageof the document, the entire document is intended, including theremaining pages of the document.

1. A method for determining a sequence of a locus of interest, saidmethod comprising: (a) amplifying a locus of interest on a template DNAusing a first and second primers, each of the first and second primerscomprising a 3′ annealing region that anneals to the template DNA,wherein the second primer contains a recognition site for a restrictionenzyme such that digestion with the restriction enzyme generates a 5′overhang containing the locus of interest, and wherein the meltingtemperature of the 3′ annealing region of the first primer is greaterthan the melting temperature of the 3′ annealing region of the secondprimer, and further wherein the annealing temperature for cycle 1 of theamplification is at about the melting temperature of the 3′ annealingregion of the second primer, the annealing temperature for cycle 2 ofthe amplification is at about the melting temperature of the 3′annealing region of the first primer, and the annealing temperature forcycle 3 is at about the melting temperature of the entire second primer,and wherein the annealing temperatures for cycle 2 and cycle 3 aregreater than the annealing temperature for cycle 1; (b) digesting theamplified DNA with the restriction enzyme that recognizes therecognition site on the second primer; (c) incorporating a nucleotideinto the digested DNA of (b) by using the 5′ overhang containing thelocus of interest as a template; and (d) determining the sequence of thelocus of interest by determining the sequence of the DNA of (c)containing the incorporated nucleotide.
 2. The method of claim 1,wherein the amplification of step (a) comprises cycles of amplificationsubsequent to cycle 3, wherein the annealing temperature of the cyclesof amplification subsequent to cycle 3 is at about the meltingtemperature of the entire second primer.
 3. The method of claim 1,wherein the template DNA is obtained from a source selected from thegroup consisting of a bacterium, fungus, virus, protozoan, plant, animaland human.
 4. The method of claim 1, wherein the template DNA isobtained from a human source.
 5. The method of claim 1, wherein thetemplate DNA is obtained from a sample selected from the groupconsisting of a cell, tissue, blood, serum, plasma, urine, spinal fluid,lymphatic fluid, semen, vaginal secretion, ascitic fluid, saliva, mucosasecretion, peritoneal fluid, fecal matter, and body exudates.
 6. Themethod of claim 1, wherein the amplification in (a) comprises polymerasechain reaction (PCR).
 7. The method of claim 1, wherein the restrictionenzyme cuts DNA at the recognition site.
 8. The method of claim 7,wherein a 5′ region of the second primer does not anneal to the templateDNA.
 9. The method of claim 7, wherein a 5′ region of the first primerdoes not anneal to the template DNA.
 10. The method of claim 7, whereinthe restriction enzyme is selected from the group consisting of BsaJ I,Bssk I, Dde I, EcoN I, Fnu4H I, and Hinf I.
 11. The method of claim 1,wherein the restriction enzyme cuts DNA at a distance from therecognition site.
 12. The method of claim 11, wherein a 5′ region of thesecond primer does not anneal to the template DNA.
 13. The method ofclaim 11, wherein a 5′ region of the first primer does not anneal to thetemplate DNA.
 14. The method of claim 11, wherein an annealing length ofthe 3′ region of the second primer is selected from the group consistingof 25-20, 20-15, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, and less than4 bases.
 15. The method of claim 11, wherein the recognition site is fora Type IIS restriction enzyme.
 16. The method of claim 15, wherein theType IIS restriction enzyme is selected from the group consisting of:Alw I, Alw26 I, Bbs I, Bbv I, BceA I, Bmr I, Bsa I, Bst71 I, BsmA I,BsmB I, BsmF I, BspM I, Ear I, Fau I, Fok I, Hga I, Ple I, Sap I, SSfaNI, and Sthi32 I.
 17. The method of claim 15, wherein the Type IISrestriction enzyme is BceA I or BsmF I.
 18. The method of claim 1,wherein the 3′ end of the second primer is adjacent to the locus ofinterest.
 19. The method of claim 1, wherein the first primer contains arecognition site for a restriction enzyme that is different from therecognition site for the restriction enzyme on the second primer. 20.The method of claim 19, further comprising digesting the DNA of (c) witha restriction enzyme that recognizes the recognition site on the firstprimer.
 21. The method of claim 1, wherein the first primer, the secondprimer, or both the first primer and the second primer contain a tag atthe 5′ terminus.
 22. The method of claim 1, wherein the first primercontains a tag at the 5′ terminus.
 23. The method of claim 22, whereinthe tag is used to separate the amplified DNA from the template DNA. 24.The method of claim 23, wherein the tag is used to separate theamplified DNA containing the incorporated nucleotide from the amplifiedDNA that does not contain the incorporated nucleotide.
 25. The method ofclaim 22, wherein the tag is selected from the group consisting of:radioisotope, fluorescent reporter molecule, chemiluminescent reportermolecule, antibody, antibody fragment, hapten, biotin, derivative ofbiotin, photobiotin, iminobiotin, digoxigenin, avidin, enzyme,acridinium, sugar, enzyme, apoenzyme, homopolymeric oligonucleotide,hormone, ferromagnetic moiety, paramagnetic moiety, diamagnetic moiety,phosphorescent moiety, luminescent moiety, electrochemiluminescentmoiety, chromatic moiety, moiety having a detectable electron spinresonance, electrical capacitance, dielectric constant, electricalconductivity, and combinations thereof.
 26. The method of claim 22,wherein the tag is biotin.
 27. The method of claim 26, wherein thebiotin tag is used to separate amplified DNA from the template DNA usinga streptavidin matrix.
 28. The method of claim 27, wherein thestreptavidin matrix is coated on wells of a microtiter plate.
 29. Themethod of claim 1, wherein the incorporation of a nucleotide in (c) isby a DNA polymerase selected from the group consisting of E. coli DNApolymerase, Klenow fragment of E. coli DNA polymerase I, T7 DNApolymerase, T4 DNA polymerase, Taq polymerase, Pfu DNA polymerase, VentDNA polymerase and sequenase.
 30. The method of claim 1, wherein theincorporation of a nucleotide in (c) comprises incorporation of alabeled nucleotide.
 31. The method of claim 30, wherein the labelednucleotide is selected from the group consisting of a dideoxynucleotidetriphosphate and deoxynucleotide triphosphate.
 32. The method of claim30, wherein the labeled nucleotide is labeled with a molecule selectedfrom the group consisting of radioactive molecule, fluorescent molecule,antibody, antibody fragment, hapten, carbohydrate, biotin, derivative ofbiotin, phosphorescent moiety, luminescent moiety,electrochemiluminescent moiety, chromatic moiety, moiety having adetectable electron spin resonance, moiety having an electricalcapacitance, moiety having a dielectric constant, and moiety having adetectable electrical conductivity.
 33. The method of claim 30, whereinthe labeled nucleotide is labeled with a fluorescent molecule.
 34. Themethod of claim 33, wherein the incorporation of a fluorescent labelednucleotide further comprises using a mixture of fluorescent andunlabeled nucleotides.
 35. The method of claim 30, wherein thedetermination of the sequence of the locus of interest in (d) comprisesdetecting labeled nucleotide.
 36. The method of claim 35, wherein thedetection is by a method selected from the group consisting of gelelectrophoresis, polyacrylamide gel electrophoresis, fluorescencedetection system, sequencing, ELISA, mass spectrometry, fluorometry,hybridization, microarray, and Southern Blot.
 37. The method of claim35, wherein the detection method is DNA sequencing.
 38. The method ofclaim 35, wherein the detection method is a fluorescence detectionsystem.
 39. The method of claim 1, wherein the incorporation of anucleotide in (c) further comprises using a mixture of labeled andunlabeled nucleotides.
 40. The method of claim 1, wherein thedetermination of the sequence of the locus of interest in (d) comprisesdetecting the nucleotide.
 41. The method of claim 1, wherein the locusof interest is suspected of containing a single nucleotide polymorphismor mutation.
 42. The method of claim 1, wherein the method is used fordetermining sequences of multiple loci of interest concurrently.
 43. Themethod of claim 42, wherein the template DNA comprises multiple locifrom a single chromosome.
 44. The method of claim 42, wherein thetemplate DNA comprises multiple loci from different chromosomes.
 45. Themethod of claim 42, wherein the loci of interest on template DNA areamplified in one reaction.
 46. The method of claim 42, wherein each ofthe loci of interest on template DNA is amplified in a separatereaction.
 47. The method of claim 46, wherein the amplified DNA arepooled together prior to digestion of the amplified DNA.
 48. The methodof claim 42, wherein each of the DNA of (c) containing the incorporatednucleotide and containing a locus of interest is separated from otherloci of interest prior to (d).
 49. The method of claim 42, wherein atleast one of the loci of interest is suspected of containing a singlenucleotide polymorphism or a mutation.
 50. A method for determining asequence of a locus of interest, said method comprising: (a) amplifyinga locus of interest on a template DNA using a first and second primers,each of the first and second primers comprising a 3′ annealing regionthat anneals to the template DNA, wherein the second primer contains arecognition site for a restriction enzyme such that digestion with therestriction enzyme generates a 5′ overhang containing the locus ofinterest, and wherein the melting temperature of the 3′ annealing regionof the first primer is greater than the melting temperature of the 3′annealing region of the second primer, and further wherein the annealingtemperature for cycle 1 of the amplification is at about the meltingtemperature of the 3′ annealing region of the second primer, and theannealing temperature for a cycle of amplification subsequent to thefirst cycle of amplification is at about the melting temperature of the3′ annealing region of the first primer, and wherein the annealingtemperature for said cycle of amplification subsequent to the firstcycle of amplification is greater than the annealing temperature forcycle 1; (b) digesting the amplified DNA with the restriction enzymethat recognizes the recognition site on the second primer; (c)incorporating a nucleotide into the digested DNA of (b) by using the 5′overhang containing the locus of interest as a template; and (d)determining the sequence of the locus of interest by determining thesequence of the DNA of (c) containing the incorporated nucleotide. 51.The method of claim 50, wherein the 5′ region of the second primer doesnot anneal to the template DNA, and further wherein in a cycle ofamplification subsequent to the cycle of amplification for which theannealing temperature is at about the melting temperature of the 3′annealing region of the first primer, the annealing temperature is atabout the melting temperature of the entire second primer.
 52. A methodfor determining a sequence of a locus of interest, said methodcomprising: (a) amplifying a locus of interest on a template DNA using afirst and second primers, each of the first and second primerscomprising a 3′ annealing region that anneals to the template DNA,wherein the second primer contains a recognition site for a restrictionenzyme that cuts DNA at a distance from the recognition site anddigestion with the restriction enzyme generates a 5′ overhang containingthe locus of interest, wherein the first primer contains a recognitionsite for a restriction enzyme that is different from the recognitionsite for the restriction enzyme on the second primer, and contains a tagat the 5′ end, and wherein the melting temperature of the 3′ annealingregion of the first primer is greater than the melting temperature ofthe 3′ annealing region of the second primer, and further wherein theannealing temperature for cycle 1 of the amplification is at about themelting temperature of the 3′ annealing region of the second primer, theannealing temperature for cycle 2 of the amplification is at about themelting temperature of the 3′ annealing region of the first primer, andthe annealing temperature for cycle 3 is at about the meltingtemperature of the entire second primer, and further wherein theannealing temperatures for cycle 2 and cycle 3 are greater than theannealing temperature for cycle 1; (b) digesting the amplified DNA withthe restriction enzyme that recognizes the recognition site on thesecond primer; (c) incorporating a labeled nucleotide into the digestedDNA of (b) by using the 5′ overhang containing the locus of interest asa template; (d) digesting the DNA of (c) with the restriction enzymethat recognizes the recognition site on the first primer; and (e)determining the sequence of the locus of interest by determining thesequence of the digested DNA of (d) containing the labeled nucleotide.53. The method of claim 52, wherein the tag is used to separate theamplified DNA from the template DNA.
 54. A method for determining asequence of a locus of interest, said method comprising: (a) amplifyinga locus of interest on a template DNA using a first and second primers,each of the first and second primers comprising a 3′ annealing regionthat anneals to the template DNA, wherein the second primer contains arecognition site for a restriction enzyme such that digestion with therestriction enzyme generates a 5′ overhang containing the locus ofinterest, wherein the 5′ region of the second primer does not anneal tothe template DNA, and wherein the annealing temperature for cycle 1 ofthe amplification is at about the melting temperature of the 3′annealing region of the second primer, and the annealing temperature fora cycle of amplification subsequent to the first cycle of amplificationis at about the melting temperature of the entire second primer, andwherein the annealing temperature for said cycle of amplificationsubsequent to the first cycle of amplification is greater than theannealing temperature for cycle 1; (b) digesting the amplified DNA withthe restriction enzyme that recognizes the recognition site on thesecond primer; (c) incorporating a nucleotide into the digested DNA of(b) by using the 5′ overhang containing the locus of interest as atemplate; and (d) determining the sequence of the locus of interest bydetermining the sequence of the DNA of (c) containing the incorporatednucleotide.